Detection of colon or breast cancer by measuring TTK polynucleotide expression

ABSTRACT

The present invention provides methods for identification of cancerous cells by detection of expression levels of TTK, as well as diagnostic, prognostic and therapeutic methods that take advantage of the differential expression of these genes in mammalian cancer. Such methods can be useful in determining the ability of a subject to respond to a particular therapy, e.g., as the basis of rational therapy. In addition, the invention provides assays for identifying pharmaceuticals that modulate activity of these genes in cancers in which these genes are involved, as well as methods of inhibiting tumor growth by inhibiting activity of TTK.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. provisional application Ser.No. 60/289,813, filed Feb. 21, 2001, which application is herebyincorporated by reference.

FIELD OF THE INVENTION

The field of the present invention relates to disease diagnosis andtreatment of cancer and identification of anti-cancer agents.

BACKGROUND OF THE INVENTION

Mitotic checkpoint genes have become widely studied for their roles indevelopment as well as for their potential role in disease such ascancer. The mitotic checkpoint involves a number of different mechanismsto ensure proper cellular division. For example, the spindle assemblycheckpoint modulates the timing of anaphase initiation in response tothe improper alignment of chromosomes at the metaphase plate. If defectsare detected, a signal is transduced to halt further progression of thecell cycle until correct bipolar attachment to the spindle is achieved.Initially identified in budding yeast, several mammalian spindlecheckpoint-associated proteins have recently been identified andpartially characterized. These proteins associate with all active humancentromeres, including neocentromeres, in the early stages of mitosisprior to the commencement of anaphase. The proteins associated with thecheckpoint protein complex (BUB1, BUBR1, BUB3, MAD2), theanaphase-promoting complex (Tsg24, p55CDC), and other proteinsassociated with mitotic checkpoint control (ERK1, 3F3/2 epitope, hZW10),were found to specifically associate with only the active centromere,suggesting that only active centromeres participate in the spindlecheckpoint. Saffery R et al., Hum Genet. 107:376-84 (2000).

Tyrosine threonine kinase (TTK), a protein kinase, phosphorylatesserine, threonine, and tyrosine hydroxyamino acids (Mills et al,. Biol.Chem. 267:16000-6 (1992)). The kinases most closely related to TTKinclude SPK1 serine, threonine, and tyrosine kinase, the Pim1, PBS2, andCDC2 serine/threonine kinases, and the TIK kinase (Mills et al. J. Biol.Chem. 267:16000-6 (1992)). The nucleotide and amino acid sequences ofhuman TTK are provided at, for example, GenBank Accession No. M86699.Expression of TTK is markedly reduced or absent in resting cells and intissues with a low proliferative index (Hogg et al. Oncogene 9:89-96(1994)). TTK mRNA is expressed in human testis, thymus, bone marrow, andother tissues that contain a large number of proliferating cells and isnot detected in tissues that contain few or no dividing cells. TTKexpression was detected in several rapidly proliferating cells lines,including various cancer cell lines. TTK expression was also detectedand in samples tissue samples from two patients with malignant ovariancancer (Mills et al., ibid.; Schmandt et al. J. Immunol. 152:96-105(1994)). TTK expression is correlated with cell proliferation, and playsa role in cell cycle control (Hogg et al., ibid.). Very low levels ofTTK mRNA and protein are present in starved cells. When cells areinduced to enter the cell cycle, levels of TTK mRNA, protein, and kinaseactivity increase at the G1/S phase of the cell cycle and peak in G2/M.TTK mRNA levels, as well as kinase activity, drop sharply in early G1,whereas protein levels are largely maintained. TTK is a human homologueof the S. cerevesiae kinase mps 1 and the S. pombe protein mph1, both ofwhich are involved in cell cycle spindle assembly checkpoint, thusindicating that TTK is a spindle checkpoint gene (see, e.g., Cahill etal. Genomics 58:181-7 (1999).

Although mitotic checkpoint impairment has been detected in humancancers (e.g., such impairment is present in about 40% of human lungcancer cell lines) mutations in the MAD mitotic checkpoint genes and theBUB gene family are infrequent. Haruki N et al., Cancer Lett.162:201-205 (2001); Mimori K et al., Oncol Rep. 8:39-42 (2001); Cahillet al., ibid.). There is thus a need for identification of mitoticcheckpoint genes that have a role in human cancers, as they can serve asinformative diagnostic and/or prognostic indicators, and therapeutictargets.

SUMMARY OF THE INVENTION

The present invention provides methods for identification of cancerouscells by detection of expression levels of TTK, as well as diagnostic,prognostic and therapeutic methods that take advantage of thedifferential expression of these genes in mammalian cancer. Such methodscan be useful in determining the ability of a subject to respond to aparticular therapy, e.g., as the basis of rational therapy. In addition,the invention provides assays for identifying pharmaceuticals thatmodulate activity of these genes in cancers in which these genes areinvolved, as well as methods of inhibiting tumor growth by inhibitingactivity of TTK.

In a first embodiment, the present invention provides a method foridentifying TTK levels in a sample of a subject suspected of havingcancer (e.g., a lung, colon, prostrate or breast tissue biopsy)comprising quantifying the level of TTK in the sample. Theidentification of increased levels of TTK in the sample provides anindication of impairment of the cell cycle checkpoint in the sampledcells.

In another embodiment, the invention provides a method for determiningthe characteristics of a malignant or pre-malignant growth comprisingdetermining (either qualitatively or quantitatively) the level of TTK inthe cells of the growth, and comparing levels with known levels invarious stages of cancer and/or normal tissue. For example, to determinethe characteristics of a particular subject's colon cancer, a sample ofthe cancer may be removed, the levels of TTK in the cancer determined,and the levels compared to normal tissue and/or levels in various stagecolon cancers derived from the same cell type. The levels of TTKidentified in the sample can thus be indicative of variouscharacteristics of the malignant or pre-malignant growth, as determinedby the characteristics of known tissue and cancers. The TTK levels canbe compared directly to the levels in other single samples, or may becompared to a standard that is derived from the data of multiplesamples.

In another embodiment, the TTK levels of a sample can be used as oneindex for determining the appropriate therapeutic intervention for asubject with a malignant or pre-malignant growth. Highly increasedlevels of TTK, for example, can be indicative of the need for moreaggressive therapy, as it is indicative of a later stage cancer.Alternatively, the level of TTK expression may be indicative of theresponsiveness of a subject to a particular pharmaceutical, and inparticular to a therapeutic intervention that affects the cancer via themitotic checkpoint.

In another embodiment, the invention features a method for identifyingagents for inhibiting growth of a tumor, particular by a breast or colontumor, by contacting a cell expressing TTK with a candidate agent, andassessing the effect of the agent upon TTK activity.

Accordingly, in one aspect the invention features a method of diagnosingcancer in a subject, the method comprising detection of TTKpolynucleotide or polypeptide in a test sample obtained from a subjectso as to determine a level of expression of the gene product; andcomparing the level of expression of the TTK in the test sample to alevel of expression in a normal cell corresponding to the same tissue;wherein detection of an expression level of TTK in the test sample thatis significantly increased from the level of expression in a normal cellindicates that the test cell is cancerous. In specific embodiments, thecancer is other than ovarian cancer, with colon cancer and breast cancerbeing of particular interest.

In another aspect, the invention features a method for determining theprognosis of a cancerous disease in a subject, the method comprisingdetecting expression of TTK in a test cell from the subject; andcomparing a level of expression of TTK in the test cell with a level ofTTK expression in a control cell; wherein the level of expression of TTKin the test cell relative to the level of expression in the control cellis indicative of the prognosis of the cancerous disease. For example,where the control cell is a normal cell, an elevated level of TTKexpression in the test cell relative to the normal cell is indicative ofthe continued presence of cancerous cells in the subject and thus arelatively poorer prognosis than where the level of TTK expression inthe test cell is at a level comparable to that found in an normal(non-cancer) cell. In specific embodiments, progress of a cancer otherthan ovarian cancer is of particular interest, especially colon andbreast cancer.

In another aspect, the invention features a method for inhibiting growthof a cancerous cell comprising introducing into a cell an antisensepolynucleotide for inhibition of TTK expression, wherein inhibition ofTTK expression inhibits replication of the cancerous cell.

In still another aspect, the invention features a method for assessingthe tumor burden of a subject, the method comprising detecting a levelof TTK expression in a test sample from a subject, the test samplesuspected of comprising increased TTK expression; wherein detection ofthe level of TTK expression in the test sample is indicative of thetumor burden in the subject, with an increased level of TTK expressionin the test sample relative to a control non-cancer cell indicates thepresence of a tumor in the subject.

In yet another aspect, the invention features a method of identifying anagent having anti-TTK activity, the method comprising contacting acancerous cell displaying elevated expression of TTK with a candidateagent; and determining the effect of the candidate agent on TTKactivity; wherein a decrease in TTK activity indicates that the agenthas anti-TTK activity. In specific embodiments, TTK activity is detectedby detecting TTK expression or by detecting a biological activity of TTK

In yet another aspect, the invention features an assay for identifying acandidate agent that inhibits growth of a cancerous cell, comprisingcontacting a cell expressing TTK polypeptide with a candidate agent; anddetecting activity of the TTK polypeptide, comparing the activity of theTTK polypeptide in the cell in the presence of the candidate agent toactivity of a TTK polypeptide in a cell in the absence of the candidateagent; wherein reduction of TTK activity in the presence of thecandidate agent relative to TTK activity in the absence of the candidateagent indicates that the candidate agent reduces TTK activity andinhibits growth of a cancerous cell.

A primary object of the invention is to exploit TTK as a therapeutictarget, e.g. by identifing candidate agents that modulate, usually thatdecrease, TTK activity in a target cell in order to, for example,inhibit cell growth.

An object of the present invention is to inhibit tumor growth byinhibition of activity of a mitotic checkpoint gene product,particularly though inhibition of TTK activity in the target tumor cell.

Another object of the invention is to facilitate rational cancertherapy. For example, where the cancer in the subject is associated withincreased TTK activity levels, a therapeutic agent is selectedaccordingly so as to facilitate reduction of TTK activity levels.

Another object of the present invention is to design clinical trialsbased on levels of TTK expression in a cancer, and more particularly todesign clinical trials based on TTK expression in combination with otherpatient attributes.

Yet another object of the invention is to identify the association ofTTK expression and intervention attributes that yield efficaciouschanges in selected disease progression measures.

An advantage of the invention is the ability to project diseaseprogression based on expression of TTK in a malignant or pre-malignantgrowth.

Another advantage of the present invention is that it allows a moresystematic approach for intervention of a cancerous disease based uponobjective indicia.

These and other objects, advantages, and features of the invention willbecome apparent to those persons skilled in the art upon reading thedetails of the methods as more fully described below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a bar graph illustrating expression of TTK in various normaltissue types as detected by PCR.

FIG. 2 is a bar graph illustrating expression of TTK in various tumorcell lines as detected by PCR.

FIGS. 3-6 are graphs illustrating expression profiles for IGF2,MAPKAPK2, TTK, and MARCKS in patients with colorectal carcinoma.

FIGS. 7 and 8 are graphs illustrating growth suppression of MDA-MB-231cells following antisense suppression of TTK expression.

FIG. 9 is a graph illustrating growth suppression of SW620 cellsfollowing antisense suppression of TTK expression.

FIG. 10 is a graph illustrating suppression of colony formation of SW620cells in soft agar following antisense suppression of TTK expression.

FIG. 11 is a graph illustrating that antisense suppression of TTK has nodetectable effect on normal immortal fibroblasts.

FIG. 12 is a bar graph illustrating induction of cell death upondepletion of TTK from SW620 cells.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

Before the present invention is described, it is to be understood thatthis invention is not limited to particular methodologies described, andas such may, of course, vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting, since the scope ofthe present invention will be limited only by the appended claims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimits of that range is also specifically disclosed. Each smaller rangebetween any stated value or intervening value in a stated range and anyother stated or intervening value in that stated range is encompassedwithin the invention. The upper and lower limits of these smaller rangesmay independently be included or excluded in the range, and each rangewhere either, neither or both limits are included in the smaller rangesis also encompassed within the invention, subject to any specificallyexcluded limit in the stated range. Where the stated range includes oneor both of the limits, ranges excluding either or both of those includedlimits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, the preferred methodsand materials are now described. All publications mentioned herein areincorporated herein by reference to disclose and describe the methodsand/or materials in connection with which the publications are cited.

It must be noted that as used herein and in the appended claims, thesingular forms “a”, “and”, and “the” include plural referents unless thecontext clearly dictates otherwise. Thus, for example, reference to “acell” includes a plurality of such cells and reference to “the agent”includes reference to one or more agents and equivalents thereof knownto those skilled in the art, and so forth.

The publications discussed herein are provided solely for theirdisclosure prior to the filing date of the present application. Nothingherein is to be construed as an admission that the present invention isnot entitled to antedate such publication by virtue of prior invention.Further, the dates of publication provided may be different from theactual publication dates which may need to be independently confirmed.

DEFINITIONS

The terms “polynucleotide” and “nucleic acid”, used interchangeablyherein, refer to a polymeric forms of nucleotides of any length, eitherribonucleotides or deoxynucleotides. Thus, these terms include, but arenot limited to, single-, double-, or multi-stranded DNA or RNA, genomicDNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine andpyrimidine bases or other natural, chemically or biochemically modified,non-natural, or derivatized nucleotide bases. These terms furtherinclude, but are not limited to, mRNA or cDNA that comprise intronicsequences (see, e.g., Niwa et al. (1999) Cell 99(7):691-702). Thebackbone of the polynucleotide can comprise sugars and phosphate groups(as may typically be found in RNA or DNA), or modified or substitutedsugar or phosphate groups. Alternatively, the backbone of thepolynucleotide can comprise a polymer of synthetic subunits such asphosphoramidites and thus can be an oligodeoxynucleoside phosphoramidateor a mixed phosphoramidate-phosphodiester oligomer. Peyrottes et al.(1996) Nucl. Acids Res. 24:1841-1848; Chaturvedi et al. (1996) Nucl.Acids Res. 24:2318-2323. A polynucleotide may comprise modifiednucleotides, such as methylated nucleotides and nucleotide analogs,uracyl, other sugars, and linking groups such as fluororibose andthioate, and nucleotide branches. The sequence of nucleotides may beinterrupted by non-nucleotide components. A polynucleotide may befurther modified after polymerization, such as by conjugation with alabeling component. Other types of modifications included in thisdefinition are caps, substitution of one or more of the naturallyoccurring nucleotides with an analog, and introduction of means forattaching the polynucleotide to proteins, metal ions, labelingcomponents, other polynucleotides, or a solid support.

The terms “polypeptide” and “protein”, used interchangeably herein,refer to a polymeric form of amino acids of any length, which caninclude coded and non-coded amino acids, chemically or biochemicallymodified or derivatized amino acids, and polypeptides having modifiedpeptide backbones. The term includes fusion proteins, including, but notlimited to, fusion proteins with a heterologous amino acid sequence,fusions with heterologous and homologous leader sequences, with orwithout N-terminal methionine residues; immunologically tagged proteins;and the like.

As used herein “TTK polynucleotide” and “TTK polypeptide” encompasspolynucleotides and polypeptides having sequence similarity or sequenceidentity to the human TTK (having GenBank accession number M86699; SEQID NO:13 and 14), or the S. cerevesiae kinase mps1 gene and geneproducts (SEQ ID NO:29 and 30), the S. pombe protein mph1 gene and geneproducts (SEQ ID NO:31 and 32), and other genes and gene productsrelated to TTK, such as SPK1 (SEQ ID NO:15 and 16), Pim1 (SEQ ID NO:17and 18), PBS2 (SEQ ID NO:19 and 20), CDC2 (SEQ ID NO:21 and 22), and TIK(SEQ ID NO:23 and 24) of at least about 65%, preferably at least about80%, more preferably at least about 85%, and can be about 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99% or more. Sequence similarity andsequence identity are calculated based on a reference sequence, whichmay be a subset of a larger sequence, such as a conserved motif, codingregion, flanking region, etc. A reference sequence will usually be atleast about 18 nt long, more usually at least about 30 nt long, and mayextend to the complete sequence that is being compared. In general,percent sequence identity is calculated by counting the number ofresidue matches (e.g., nucleotide residue or amino acid residue) betweenthe query and test sequence and dividing total number of matches by thenumber of residues of the individual sequences found in the region ofstrongest alignment. Thus, where 10 residues of an 11 residue querysequence matches a test sequence, the percent identity above would be 10divided by 11, or approximately, 90.9%. Algorithms for computer-basedsequence analysis are known in the art, such as BLAST (see, e.g.,Altschul et al., J. Mol. Biol., 215:403-10 (1990)), particularly theSmith-Waterman homology search algorithm as implemented in MPSRCHprogram (Oxford Molecular). For the purposes of this invention, apreferred method of calculating percent identity is the Smith-Watermanalgorithm, using the following. Global DNA sequence identity must begreater than 65% as determined by the Smith-Waterman homology searchalgorithm as implemented in MPSRCH program (Oxford Molecular) using anaffine gap search with the following search parameters: gap openpenalty, 12; and gap extension penalty, 1. The human TTK cDNA isrepresented by the polynucleotide sequence of SEQ ID NO:13 and the humanTTK polypeptide is represented by the sequence of SEQ ID NO:14.

“Antisense polynucleotide” or “antisense oligonucleotide” are usedinterchangeably herein to mean an unmodified or modified nucleic acidhaving a nucleotide sequence complementary to a given polynucleotidesequence (e.g., a polynucleotide sequence encoding. TTK) includingpolynucleotide sequences associated with the transcription ortranslation of the given polynucleotide sequence (e.g., a promoter of apolynucleotide encoding TTK), where the antisense polynucleotide iscapable of hybridizing to a TTK-encoding polynucleotide sequence. Ofparticular interest are antisense polynucleotides capable of inhibitingtranscription and/or translation of a TTK-encoding polynucleotide eitherin vitro or in vivo.

The term “cDNA” as used herein is intended to include all nucleic acidsthat share the arrangement of sequence elements found in native maturemRNA species, where sequence elements are exons (e.g., sequencesencoding open reading frames of the encoded polypeptide) and 3′ and 5′non-coding regions. Normally mRNA species have contiguous exons, withthe intervening introns removed by nuclear RNA splicing to create acontinuous open reading frame encoding TTK.

A “variant” as used in the context of a “variant polypeptide” refers toan amino acid sequence that is altered by one or more amino acidsrelative to a reference amino acid sequence. The variant can have“conservative” changes, wherein a substituted amino acid has similarstructural or chemical properties, e.g., replacement of leucine withisoleucine. More rarely, a variant can have “nonconservative” changes,e.g., replacement of a glycine with a tryptophan. Similar minorvariations can also include amino acid deletions or insertions, or both.Guidance in determining which and how many amino acid residues may besubstituted, inserted, or deleted without abolishing biological orimmunological activity can be found using computer programs well knownin the art, for example, DNAStar software.

A “deletion” is defined as a change in either amino acid or nucleotidesequence in which one or more amino acid or nucleotide residues,respectively, are absent as compared to reference amino acid sequence ornucleotide sequence. Deletions can be of any length, but are preferablyapproximately 50, 20, 15, 10, 5 or 3 amino acids or nucleotides inlength.

An “insertion” or “addition” is that change in an amino acid ornucleotide sequence which has resulted in the addition of one or moreamino acid or nucleotide residues, respectively, as compared to areference amino acid sequence or nucleotide sequence. Insertions oradditions can be of any length, but are preferably approximately 50, 20,15, 10, 5 or 3 amino acids or nucleotides in length.

A “substitution” results from the replacement of one or more amino acidsor nucleotides by different amino acids or nucleotides, respectively, ascompared to a reference amino acid sequence or nucleotide sequence.Substitutions can be of any length, but are preferably approximately 50,20, 15, 10, 5 or 3 amino acids or nucleotides in length.

The terms “single nucleotide polymorphism” and “SNP” refer topolymorphisms of a single base change relative to a reference sequence.

The term “biologically active” refers to gene product, usually apolypeptide, having structural, regulatory, or biochemical functions ofa naturally occurring gene product, e.g., protein. “Immunologicallyactive” defines the capability of the natural, recombinant, or syntheticpolypeptide, or any oligopeptide thereof, to elicit a specific immuneresponse in appropriate animals or cells and to bind with specificantibodies.

The term “derivative” as used herein refers to the chemical modificationof a nucleic acid or amino acid sequence relative to a reference nucleicacid or amino acid sequence. Illustrative of such modifications would bereplacement of hydrogen by an alkyl, acyl, or amino group. A nucleicacid derivative generally encodes a polypeptide which retains essentialbiological characteristics of the polypeptide encoded by the referencenucleic acid (e.g., the “parent” molecule).

As used herein the term “isolated” is meant to describe a compound ofinterest (e.g., either a polynucleotide or a polypeptide) that is in anenvironment different from that in which the compound naturally occurs.“Isolated” is meant to include compounds that are within samples thatare substantially enriched for the compound of interest and/or in whichthe compound of interest is partially or substantially purified.

As used herein, the term “substantially purified” refers to a compound(e.g., either a polynucleotide or a polypeptide) that is removed fromits natural environment and is at least 60% free, preferably 75% free,and most preferably 90% free from other components with which it isnaturally associated.

“Stringency” typically occurs in a range from about Tm −5° C. (5° C.below the Tm of the probe or antibody) to about 20° C. to 25° C. belowTm. As will be understood by those of skill in the art, a stringencyhybridization can be used to identify or detect identical polynucleotidesequences or to identify or detect similar or related polynucleotidesequences.

The term “hybridization” as used herein shall include “any process bywhich a strand of nucleic acid joins with a complementary strand throughbase pairing” (Coombs, Dictionary of Biotechnology, Stockton Press, NewYork N.Y. (1994)). Amplification as carried out in the polymerase chainreaction technologies is described in Dieffenbach et al., PCR Primer, aLaboratory Manual, Cold Spring Harbor Press, Plainview N.Y. (1995).

The term “transformation” as used herein refers to a permanent ortransient genetic change, induced in a cell following incorporation ofnew DNA (ie., DNA exogenous to the cell). Genetic change can beaccomplished either by incorporation of the new DNA into the genome ofthe host cell, or by transient or stable maintenance of the new DNA asan episomal element. Where the cell is a mammalian cell, a permanentgenetic change is generally achieved by introduction of the DNA into thegenome of the cell.

The term “construct” as used herein refers to a recombinant nucleicacid, generally recombinant DNA, that has been generated for the purposeof the expression of a specific nucleotide sequence(s), or is to be usedin the construction of other recombinant nucleotide sequences.

As used herein, the term “differentially expressed” generally refers toa polynucleotide that is expressed at levels in a test cell that differsignificantly from levels in a reference cell, e.g., mRNA is found atlevels at least about 25%, at least about 50% to about 75%, at leastabout 90% increased or decreased, generally at least about 1.2-fold, atleast about 1.5-fold, at least about 2-fold, at least about 5-fold, atleast about 10-fold, or at least about 50-fold or more increased ordecreased in a cancerous cell when compared with a cell of the same typethat is not cancerous. The comparison can be made between two tissues,for example, if one is using in situ hybridization or another assaymethod that allows some degree of discrimination among cell types in thetissue. The comparison may also be made between cells removed from theirtissue source. “Differential expression” refers to both quantitative, aswell as qualitative, differences in the genes' temporal and/or cellularexpression patterns among, for example, normal and neoplastic tumorcells, and/or among tumor cells which have undergone different tumorprogression events.

The terms “correspond to” or “represents” as used in, for example, thephrase “polynucleotide corresponds to a differentially expressed gene”are used to refer to the relationship between a given polynucleotide andthe gene from which the polynucleotide sequence is derived (e.g., apolynucleotide that is derived from a coding region of the gene, asplice variant of the gene, an exon, and the like) or to which thepolynucleotide hybridizes to under stringer conditions.

“Differentially expressed polynucleotide” as used herein refers to anucleic acid molecule (RNA or DNA) comprising a sequence that representsor corresponds to a differentially expressed gene, e.g., thedifferentially expressed polynucleotide comprises a sequence (e.g., anopen reading frame encoding a gene product; a non-coding sequence) thatuniquely identifies a differentially expressed gene so that detection ofthe differentially expressed polynucleotide in a sample is correlatedwith the presence of a differentially expressed gene in a sample.“Differentially expressed polynucleotides” is also meant to encompassfragments of the disclosed polynucleotides, e.g., fragments retainingbiological activity, as well as nucleic acids homologous, substantiallysimilar, or substantially identical (e.g., having about 90% sequenceidentity) to the disclosed polynucleotides.

“Diagnosis” as used herein generally includes determination of asubject's susceptibility to a disease or disorder, determination as towhether a subject is presently affected by a disease or disorder,prognosis of a subject affected by a disease or disorder (e.g.,identification of pre-metastatic or metastatic cancerous states, stagesof cancer, or responsiveness of cancer to therapy), and therametrics(e.g., monitoring a subject's condition to provide information as to theeffect or efficacy of therapy).

As used herein, the term “a polypeptide associated with cancer” (e.g.,as in polypeptide associated with colon cancer) refers to a polypeptidethat is present at relatively higher or lower levels in a cancer cellrelative to a normal cell of the same type.

The term “biological sample” encompasses a variety of sample typesobtained from an organism and can be used in a diagnostic or monitoringassay. The term encompasses blood and other liquid samples of biologicalorigin, solid tissue samples, such as a biopsy specimen or tissuecultures or cells derived therefrom and the progeny thereof. The termencompasses samples that have been manipulated in any way after theirprocurement, such as by treatment with reagents, solubilization, orenrichment for certain components. The term encompasses a clinicalsample, and also includes cells in cell culture, cell supernatants, celllysates, serum, plasma, biological fluids, and tissue samples.

The terms “treatment”, “treating”, “treat” and the like are used hereinto generally refer to obtaining a desired pharmacologic and/orphysiologic effect. The effect may be prophylactic in terms ofcompletely or partially preventing a disease or symptom thereof and/ormay be therapeutic in terms of a partial or complete stabilization orcure for a disease and/or adverse effect attributable to the disease.“Treatment” as used herein covers any treatment of a disease in amammal, particularly a human, and includes: (a) preventing the diseaseor symptom from occurring in a subject which may be predisposed to thedisease or symptom but has not yet been diagnosed as having it; (b)inhibiting the disease symptom, i.e., arresting its development; orrelieving the disease symptom, i.e., causing regression of the diseaseor symptom. Thus “treatment of cancer” thus encompasses one or more ofinhibition of cellular proliferation, inhibition of metastasis, and thelike.

The terms “individual,” “subject,” “host,” and “patient,” usedinterchangeably herein and refer to any mammalian subject for whomdiagnosis, treatment, or therapy is desired, particularly humans. Othersubjects may include cattle, dogs, cats, guinea pigs, rabbits, rats,mice, horses, and so on.

The phrase “specific binding pair” as used herein comprises a specificbinding member and a binding partner which have a particular specificityfor each other and which bind to each other in preference to othermolecules under stringent conditions. Examples of specific binding pairsare antigens and antibodies, molecules and receptors and complementarynucleotide sequences. Other examples of binding pairs will be apparentto one skilled in the art upon reading the present disclosure. Further,the term “specific binding pair” is also applicable where either or bothof the specific binding member and the binding partner comprise a partof a larger molecule. In embodiments in which the specific binding pairare nucleic acid sequences, they are preferably between 10 to 200nucleotides long, more preferably greater than 15 to 100 nucleotideslong.

By “antibody” is meant an immunoglobulin protein which is capable ofbinding an antigen. Antibody as used herein is meant to include theentire antibody as well as any antibody fragments (e.g., F(ab′)₂, Fab′,Fab, Fv) capable of binding the epitope, antigen, or antigenic fragmentof interest.

Antibodies of the invention are immunoreactive or immunospecific for andtherefore specifically and selectively bind to a protein of interest,e.g., human TTK protein. Antibodies which are immunoreactive andimmunospecific for human TTK are preferred. Antibodies for human TTK arepreferably immunospecific—i.e., not substantially cross-reactive withrelated materials, although they may recognize TTK homologs acrossspecies. The term “antibody” encompasses all types of antibodies (e.g.,monoclonal and polyclonal).

By “binds specifically” is meant high avidity and/or high affinitybinding of an antibody to a specific polypeptide, e.g., epitope of a TTKprotein. Antibody binding to its epitope on this specific polypeptide isstronger than binding of the same antibody to any other epitope,particularly those which may be present in molecules in associationwith, or in the same sample, as the specific polypeptide of interest.Antibodies which bind specifically to a polypeptide of interest may becapable of binding other polypeptides at a weak, yet detectable, level(e.g., 10% or less of the binding shown to the polypeptide of interest).Such weak binding, or background binding, is readily discernible fromthe specific antibody binding to the compound or polypeptide ofinterest, e.g., by use of appropriate controls.

The terms “cancer”, “neoplasm”, “tumor”, and the like are usedinterchangeably herein to refer to cells which exhibit relativelyautonomous growth, so that they exhibit an aberrant growth phenotypecharacterized by a significant loss of control of cell proliferation. Ingeneral, cells of interest for detection or treatment in the presentapplication include pre-malignant (e.g., benign hyperplasiac),malignant, metastatic, and non-metastatic cells.

“TTK activity” as used herein refers to activity of the TTK polypeptidein phosphorylation of a recipient substrate.

“Modulation of TTK activity” as used herein refers to an increase ordecrease in TTK activity that can be a result of, for example,interaction of an agent with a TTK polypeptide (e.g., reversible orirreversible binding of an inhibitory agent so as to interfere with TTKpolypeptide interaction with a donor molecule or a recipient (acceptor)molecule in the phosphorylation activity of TTK), inhibition of TTKtranscription and/or translation (e.g., through antisense interactionwith the TTK gene or TTK transcript, through modulation of transcriptionfactors that facilitate TTK expression), and the like. Modulation of TTKactivity that results in a decrease of TTK activity is of particularinterest in the invention. In this context, TTK activity can bedecreased by an inhibitory agent at least 10%, 25%, 50%, 75%, 85%, 90%,up to 100% relative to TTK activity in the absence of an agent. TTKactivity can be assessed by assaying enzymatic activity, by assessingTTK polypeptide levels, or by assessing TTK transcription levels.Comparisons of TTK activity can also be accomplished by comparing TTKactivity assessed (either qualitatively or quantitatively) in a testsample to a standard TTK activity (e.g., a level of TTK activity in theabsence of an inhibitory agent or agonist, that is associated with anormal cell, a level of TTK activity of a cancerous cell of a selectedtissue type, and the like).

Overview

Human TTK is a mitotic checkpoint gene which encodes an 857 amino acidprotein that exhibits activity of a mixed specificity (tyr/thr) kinase.TTK is expressed in rapidly proliferating tissues such as testis andthymus. See, e.g., Mills GB et al., J. Biol. Chem. 267:16000-6 (1992).The present invention is based upon the finding that TTK isdifferentially expressed in colon tumor cells relative to normal coloncells as detected by microarray analysis. Differential expression wasconfirmed in cell lines derived from various forms of cancer, indicatingthat the involvement of TTK in cancer as a more general mechanism. Inaddition, disruption of TTK function using antisense oligonucleotides to“knock-out” TTK message decreased proliferation, inhibited anchorageindependent growth, and induced apoptosis of cancer cell lines,including a metastatic breast cancer cell line (MDA-MB-213) and acolorectal carcinoma cell line (SW620). These data indicate that TTK canbe a therapeutic target for chemotherapy in cancers in which TTK isoverexpressed.

The identification of the association of TTK with cancer, and theconfirmation that inhibition of TTK activity (e.g., by reducing TTKexpression) serves as the basis for the materials and methods of theinvention, such as are disclosed and discussed herein, for use in, forexample, diagnosing cancer of a patient, particularly a cancer that issusceptible to treatment by decreasing activity of TTK. The inventionalso provides for planning and selection of appropriate therapeuticand/or prophylactic treatment, permitting streamlining of treatment bytargeting those most likely to benefit. The invention also provides fortreatment of a cancer associated with aberrant TTK levels (e.g.,associated with overexpression or overproduction of TTK), e.g. byinhibition of gene product production (e.g., decreasing levels oftranscription and/or translation), by decreasing TTK activity (e.g., bydecreasing TTK gene product production (e.g., at the level oftranscription or translation) and/or by reducing one or more of TTK'skinase activities).

Various aspects of the invention will now be described in more detail.

Diagnostic Methods

In one aspect the invention is based on the discovery that TTK activityis present at higher levels in cancerous cells (particularly in coloncancer and breast cancer) than in normal cells of the same cell type.This discovery serves as the basis for identification of cancerouscells, as well as identification of tumors that are susceptible totherapy by inhibiting activity of TTK, e.g., by inhibiting TTKexpression at the level of transcription or translation or both, byinhibiting TTK activity, and the like.

TTK gene products e.g. TTK encoding mRNA or TTK polypeptides are ofparticular interest as markers (e.g., in bodily fluids (such as blood)or in tissues) to detect the earliest changes along the carcinogenesispathway (e.g., to differentiate cancerous tissue from non-canceroustissue) and/or to monitor the efficacy of various therapies andpreventive interventions. For example, a relatively increased level ofexpression of TTK compared to normal cells or tissues of the same typecan be indicative of a poorer prognosis, and therefore warrant moreaggressive therapy (e.g., chemo- or radio-therapy) for a patient or viceversa. The correlation of surrogate tumor specific features withresponse to treatment and outcome in patients can define prognosticindicators that allow the design of tailored therapy based on themolecular profile of the tumor. These therapies include antibodytargeting, antagonists (e.g., small molecules), and gene therapy.Determining TTK expression and comparison of a patients profile withknown expression in normal tissue and variants of the disease allows adetermination of the best possible treatment for a patient, both interms of specificity of treatment and in terms of comfort level of thepatient. Surrogate tumor markers, such as polynucleotide expression, canalso be used to better classify, and thus diagnose and treat, differentforms and disease states of cancer. Two classifications widely used inoncology that can benefit from identification of TTK expression levelsare staging of the cancerous disorder, and grading the nature of thecancerous tissue.

TTK polynucleotides, as well as their encoded gene products, can beuseful to monitor patients having or susceptible to cancer to detectpotentially malignant events at a molecular level before they aredetectable at a gross morphological level. In addition, detection of TTKgene products can be useful as therametrics, e.g., to assess theeffectiveness of therapy by using the polynucleotides or their encodedgene products, to assess, for example, tumor burden in the patientbefore, during, and after therapy.

Furthermore, a polynucleotide identified as corresponding to a gene thatis differentially expressed in, and thus is important for, one type ofcancer can also have implications for development or risk of developmentof other types of cancer, e.g., where a polynucleotide represents a genedifferentially expressed across various cancer types. Thus, for example,expression of a polynucleotide corresponding to a gene that has clinicalimplications for metastatic colon cancer can also have clinicalimplications for stomach cancer or endometrial cancer.

In making a diagnosis, prognosis, risk assessment, or measurement oftumor burden based on the enzymatic activity of TTK or the expressionlevels of TTK polypeptide or TTK encoding polynucleotides, activity orexpression levels may be compared to those of suitable cancerous ornon-cancerous control samples. For example, a diagnosis of cancer can bemade if TTK activity is increased at by 25%, 50%, 75%, 90%, up to 100%,or, alternatively by 5-fold, 10-fold, 50-fold, or more than 100-foldrelative to a normal non-cancerous cell of the same tissue type.

Other gene products that are differentially expressed in cancerous cellsrelative to, for example, non-cancer cells of between cancer cells ofdiffering malignant potential (e.g., non-malignant tumor cells versuscells of high potential malignancy) can also be assayed in addition toTTK for differential expression in a test cell. Such exemplary geneproducts include, but are not necessarily limited to MAPKAP kinase 2(SEQ ID. No. 33 and 34), MARCKS (SEQ ID NO:35 and 36) and/or IGF2 (SEQID NO:37 and 38).

Staging. Staging is a process used by physicians to describe howadvanced the cancerous state is in a patient. Staging assists thephysician in determining a prognosis, planning treatment and evaluatingthe results of such treatment. Staging systems vary with the types ofcancer, but generally involve the following “TNM” system: the type oftumor, indicated by T; whether the cancer has metastasized to nearbylymph nodes, indicated by N; and whether the cancer has metastasized tomore distant parts of the body, indicated by M. Generally, if a canceris only detectable in the area of the primary lesion without havingspread to any lymph nodes it is called Stage I. If it has spread only tothe closest lymph nodes, it is called Stage II. In Stage II, the cancerhas generally spread to the lymph nodes in near proximity to the site ofthe primary lesion. Cancers that have spread to a distant part of thebody, such as the liver, bone, brain or other site, are Stage IV, themost advanced stage.

The differential expression level of TTK can facilitate fine-tuning ofthe staging process by identifying markers for the aggressiveness of acancer, e.g. the metastatic potential, as well as the presence indifferent areas of the body. Thus, a Stage II cancer with a largedifferential level of expression of TTK can signify a cancer with a highmetastatic potential and can be used to change a borderline Stage IItumor to a Stage III tumor, justifying more aggressive therapy.

Grading of cancers. Grade is a term used to describe how closely a tumorresembles normal tissue of its same type. The microscopic appearance ofa tumor is used to identify tumor grade based on parameters such as cellmorphology, cellular organization, and other markers of differentiation.As a general rule, the grade of a tumor corresponds to its rate ofgrowth or aggressiveness, with undifferentiated or high-grade tumorsgenerally being more aggressive than well differentiated or low-gradetumors. The following guidelines are generally used for gradingtumors: 1) GX Grade cannot be assessed; 2) G1 Well differentiated; G2Moderately well differentiated; 3) G3 Poorly differentiated; 4) G4Undifferentiated. TTK activity levels (e.g., expression levels) can beespecially valuable in determining the grade of the tumor, as they notonly can aid in determining the differentiation status of the cells of atumor, they can also identify factors other than differentiation thatare valuable in determining the aggressiveness of a tumor, such asmetastatic potential.

Detection of colon cancer. Polynucleotides and polypeptidescorresponding to TTK can be used to detect colon cancer in a subject.Colorectal cancer is one of the most common neoplasms in humans andperhaps the most frequent form of hereditary neoplasia. Prevention andearly detection are key factors in controlling and curing colorectalcancer. Colorectal cancer begins as polyps, which are small, benigngrowths of cells that form on the inner lining of the colon. Over aperiod of several years, some of these polyps accumulate additionalmutations and become cancerous. Multiple familial colorectal cancerdisorders have been identified, which are summarized as follows: 1)Familial adenomatous polyposis (FAP); 2) Gardner's syndrome; 3)Hereditary nonpolyposis colon cancer (HNPCC); and 4) Familial colorectalcancer in Ashkenazi Jews. The expression of appropriate polypeptide andpolynucleotides can be used in the diagnosis, prognosis and managementof colorectal cancer. Detection of colon cancer can be determined usingexpression levels of TTK alone or in combination with the levels ofexpression of other genes differentially expressed in colon cancer.Determination of the aggressive nature and/or the metastatic potentialof a colon cancer can be determined by comparing levels of TTK with alevel associated with a normal cell, and comparing total levels ofanother sequence known to be differentially expressed, or otherwise be amarker of, cancerous tissue, e.g., expression of p53, DCC, ras, FAP(see, e.g., Fearon E R, et al., Cell (1990) 61(5):759; Hamilton S R etal., Cancer (1993) 72:957; Bodmer W, et al., Nat Genet. (1994) 4(3):217;Fearon E R, Ann N Y Acad Sci. (1995) 768:101) or MAPKAP kinase 2 (SEQID. No. 33 and 34), MARCKS (SEQ ID NO:35 and 36) and/or IGF2 (SEQ IDNO:37 and 38). For example, development of colon cancer can be detectedby examining the level of expression of a gene corresponding to apolynucleotides described herein to the levels of oncogenes (e.g. ras)or tumor suppressor genes (e.g. FAP or p53). Thus expression of specificmarker polynucleotides can be used to discriminate between normal andcancerous colon tissue, to discriminate between colon cancers withdifferent cells of origin, to discriminate between colon cancers withdifferent potential metastatic rates, etc. For a review of markers ofcancer, see, e.g., Hanahan et al. (2000) Cell 100:57-70.

Detection of breast cancer. The majority of breast cancers areadenocarcinomas subtypes, which can be summarized as follows: 1) ductalcarcinoma in situ (DCIS), including comedocarcinoma; 2) infiltrating (orinvasive) ductal carcinoma (IDC); 3) lobular carcinoma in situ (LCIS);4) infiltrating (or invasive) lobular carcinoma (ILC); 5) inflammatorybreast cancer; 6) medullary carcinoma; 7) mucinous carcinoma; 8) Paget'sdisease of the nipple; 9) Phyllodes tumor; and 10) tubular carcinoma.

The expression levels of TTK can be used in the diagnosis and managementof breast cancer, as well as to distinguish between types of breastcancer. Detection of breast cancer can be determined using expressionlevels of TTK, either alone or in combination with expression of othergene known to be differentially expressed in breast cancer.Determination of the aggressive nature and/or the metastatic potentialof a breast cancer can also be determined by comparing levels of TTK andcomparing levels of another sequence known to vary in cancerous tissue,e.g. ER expression. In addition, development of breast cancer can bedetected by examining the ratio of expression of TTK to the levels ofsteroid hormones (e.g., testosterone or estrogen) or to other hormones(e.g., growth hormone, insulin). Thus expression of specific markerpolynucleotides and polypeptides can be used to discriminate betweennormal and cancerous breast tissue, to discriminate between breastcancers with different cells of origin, to discriminate between breastcancers with different potential metastatic rates, etc.

Detection Methods

A number of methods are known in the art for analyzing biologicalsamples from individuals to determine whether the individual hasincreased expression of a TTK gene product (e.g., RNA or protein) bydetecting the TTK gene product in a biological sample from that subject.As discussed above, the purpose of such analysis may be used fordiagnosis, to detect the presence of an existing cancer, to helpidentify the type of cancer, to assist a physician in determining theseverity or likely course of the cancer, and/or to optimize treatment ofit. In specific non-limiting embodiments, the methods are useful fordetecting cancer cells, facilitating diagnosis of cancer and theseverity of a cancer (e.g., tumor grade, tumor burden, and the like) ina subject, facilitating a determination of the prognosis of a subject,and assessing the responsiveness of the subject to therapy (e.g., byproviding a measure of therapeutic effect through, for example,assessing tumor burden during or following a chemotherapeutic regimen).In additional embodiments, the methods are useful for classification orstratification of cancer cells, e.g., for the purpose of selectingpatients to be included in a clinical trial population, for selecting anappropriate therapy (e.g., selecting therapy according to an expressionprofile of the cancerous cells), and the like.

Kits

The detection methods can be provided as part of a kit. Thus, theinvention further provides kits for detecting the presence and/or alevel of TTK activity e.g., by detection of a TTK-encoding mRNA and/or apolypeptide encoded thereby or by measuring TTK activity, in abiological sample. Procedures using these kits can be performed byclinical laboratories, experimental laboratories, medical practitioners,or private individuals. The kits of the invention for detecting TTKpolypeptide that is differentially expressed in cancer cells comprise amoiety that specifically binds the polypeptide, which may be a specificantibody. The kits of the invention for detecting a TTK-encodingpolynucleotide that is differentially expressed in cancer cells comprisea moiety that specifically hybridizes to such a polynucleotide such as aprimer. The kits of the invention for detecting TTK activity comprise arecipient substrate capable of being phosphorylated by TTK, and alabeled donor substrate. The kits may optionally provide additionalcomponents that are useful in the procedure, including, but not limitedto, buffers, developing reagents, labels, reacting surfaces, means fordetection, control samples, standards, instructions, and interpretiveinformation.

Screening for TTK Nucleic Acid or Polypeptide

Methods for detection of TTK activity include screening for the presenceof TTK nucleic acid sequences representing an expressed TTK gene oralleles or variants thereof, and detecting the TTK polypeptide. Themethods make use of biological samples from individuals that aresuspected of contain the nucleic acid sequences or polypeptide. Examplesof biological samples include blood, plasma, serum, tissue samples,tumor samples, saliva and urine.

Exemplary approaches for detecting TTK nucleic acid or polypeptidesinclude: (a) determining the presence of the polypeptide encoded by theTTK gene; (b) using a specific binding member capable of binding to aTTK nucleic acid sequence (e.g., a known complementary sequence), thespecific binding member comprising a nucleic acid that hybridizes withthe TTK sequence under stringent conditions (c) using a substancecomprising an antibody domain with specificity for a TTK nucleic acidsequence or the polypeptide encoded by it, the specific binding memberbeing labeled to allow detection of the specific binding member to itsbinding partner is detectable; (d) using PCR involving one or moreprimers to determine relative levels of TTK in a sample from a patient;and (e) using an assay for TTK activity, e.g., phosphorylation of a TTKsubstrate.

The determination of TTK levels can include both levels of normal TTKand/or variant forms of TTK. A variant form of the gene may contain oneor more insertions, deletions, substitutions and/or additions of one ormore nucleotides compared with the wild-type sequence which may or maynot alter the gene function. Differences at the nucleic acid level arenot necessarily reflected by a difference in the amino acid sequence ofthe encoded polypeptide due to the degeneracy of the genetic code.However, a mutation or other difference in a gene may result in aframe-shift or stop codon, which could seriously affect the nature ofthe polypeptide produced (if any), or a point mutation or grossmutational change to the encoded polypeptide, including insertion,deletion, substitution and/or addition of one or more amino acids orregions in the polypeptide.

A mutation in a promoter sequence or other regulatory region may alter(e.g., reduce or enhance) expression from the gene or affect theprocessing or stability of the mRNA transcript.

There are various methods for detecting a particular nucleic acidsequence in a test sample. Tests may be carried out on preparationscontaining mRNA or cDNA generated from isolated mRNA in a manner thatreflects the relative levels of mRNA transcripts in the sample. Levelsof RNA can be determined specific amplification reaction such as PCRusing one or more pairs of primers may be employed to amplify a regionof the nucleic acid, and preferably a region with less homology to othergenes. Nucleic acid for testing may be prepared from nucleic acidremoved from cells or in a library using a variety of other techniquessuch as restriction enzyme digest and electrophoresis.

Nucleic acid may be screened using a TTK-specific probe. Such a probecorresponds in sequence to a region of the TTK gene, or its complement.Under stringent conditions, specific hybridization of such a probe totest nucleic acid is indicative of the presence of the TTK nucleic acidin a sample. For efficient screening purposes, more than one probe maybe used on the same test sample. The probe may contain as few as 15, 20,50 or 100 nucleotides of the TTK gene of SEQ ID. No. 13 or may be aslong as or 500, 1 kb or as much as 3.8 kb or longer in length.

Allele- or variant-specific oligonucleotides may similarly be used inPCR to specifically amplify particular sequences if present in a testsample. Assessment of whether a PCR band contains a gene variant may becarried out in a number of ways familiar to those skilled in the art.The PCR product may for instance be treated in a way that enables one todisplay the mutation or polymorphism on a denaturing polyacrylamide DNAsequencing gel, with specific bands that are linked to the gene variantsbeing selected. This can be done simultaneous to or sequentially todetermining the level of a normal TTK sequence, e.g., to determine thecombinatory levels of total TTK.

The presence of absence of a lesion in a promoter or other regulatorysequence may also be assessed by determining the level of mRNAproduction by transcription or the level of polypeptide production bytranslation from the mRNA. The presence of differences in sequence ofnucleic acid molecules may be detected by means of restriction enzymedigestion, such as in a method of DNA fingerprinting where therestriction pattern produced when one or more restriction enzymes areused to cut a sample of nucleic acid is compared with the patternobtained when a sample containing the normal gene or a variant or alleleis digested with the same enzyme or enzymes.

A test sample of nucleic acid may be provided for example by extractingnucleic acid from cells, e.g., cells from a tumor biopsy.

Detection of TTK Polypetptides

There are various methods for determining the presence or absence in atest sample of a TTK polypeptide. A sample may be tested for thepresence of a binding partner for a specific binding member such as anantibody (or mixture of antibodies), specific for wild-type TTK and/orone or more particular variants (e.g., allelic variants) of the TTKpolypeptide. In such cases, the sample may be tested by being contactedwith a specific binding member such as an antibody under appropriateconditions for specific binding. Where a panel of antibodies is used,different reporting labels may be employed for each antibody so thatbinding of each can be determined. In addition to detection of TTKpolypeptides using anti-TTK antibodies, TTK polypeptide can also beidentified using TTK-specific activity assays.

Arrays

Binding agents (such as antibodies or nucleic acid sequences) can alsobe immobilized in small, discrete locations and/or as arrays on solidsupports or on diagnostic chips. These approaches can be particularlyvaluable as they can provide great sensitivity, particularly through theuse of fluorescently labeled reagents, require only very small amountsof biological sample from individuals being tested and allow a varietyof separate assays can be carried out simultaneously. This latteradvantage can be useful as it provides an assay for different proteins(e.g., an oncogene or tumor suppressor) in tandem with the assay forTTK. Thus, in a further aspect, the present invention provides a supportor diagnostic chip having immobilized thereon one or more binding agentscapable of specifically binding TTK nucleic acid or polypeptides,optionally in combination with other reagents needed to carrying out anassay.

Methods for Expression of TTK Polypeptide

The full-length or partial polypeptides encoded by TTK may be expressedin any expression system, including, for example, bacterial, yeast,insect, amphibian and mammalian systems. Suitable vectors and host cellsfor which are described in U.S. Pat. No. 5,654,173. Appropriatepolynucleotide constructs are purified using standard recombinant DNAtechniques as described in, for example, Sambrook et al., (1989)Molecular Cloning: A Laboratory Manual, 2nd ed. (Cold Spring HarborPress, Cold Spring Harbor, N.Y.), and under current regulationsdescribed in United States Dept. of HHS, National Institute of Health(NIH) Guidelines for Recombinant DNA Research.

Bacteria. Expression systems in bacteria include those described inChang et al., Nature (1978) 275:615, Goeddel et al., Nature (1979)281:544, Goeddel et al., Nucleic Acids Res. (1980) 8:4057; EP 0 036,776,U.S. Pat. No. 4,551,433, DeBoer et al., Proc. Natl. Acad. Sci. (USA)(1983) 80:21-25, and Siebenlist et al., Cell (1980) 20:269.

Yeast. Expression systems in yeast include those described in Hinnen etal., Proc. Natl. Acad. Sci. (USA) (1978) 75:1929; Ito et al., J.Bacteriol. (1983) 153:163; Kurtz et al., Mol. Cell. Biol. (1986) 6:142;Kunze et al., J. Basic Microbiol. (1985) 25:141; Gleeson et al., J. Gen.Microbiol. (1986) 132:3459, Roggenkamp et al., Mol. Gen. Genet. (1986)202:302) Das et al., J. Bacteriol. (1984) 158:1165; De Louvencourt etal., J. Bacteriol. (1983) 154:737, Van den Berg et al., Bio/Technology(1990) 8:135; Kunze et al., J. Basic Microbiol. (1985) 25:141; Cregg etal., Mol. Cell. Biol. (1985) 5:3376, U.S. Pat. Nos. 4,837,148 and4,929,555; Beach and Nurse, Nature (1981) 300:706; Davidow et al., Curr.Genet. (1985) 10:380, Gaillardin et al., Curr. Genet. (1985)10:49,Ballance et al., Biochem. Biophys. Res. Commun. (1983) 112:284-289;Tilburn et al., Gene (1983) 26:205-221, Yelton et al., Proc. Natl. Acad.Sci. (USA) (1984) 81:1470-1474, Kelly and Hynes, EMBO J. (1985)4:475479; EP 0 244,234, and WO 91/00357.

Insect Cells. Expression of heterologous genes in insects isaccomplished as described in U.S. Pat. No. 4,745,051, Friesen et al.(1986) “The Regulation of Baculovirus Gene Expression” in: The MolecularBiology Of Baculoviruses (W. Doerfler, ed.), EP 0 127,839, EP 0 155,476,and Vlak et al., J. Gen. Virol. (1988) 69:765-776, Miller et al., Ann.Rev. Microbiol. (1988) 42:177, Carbonell et al., Gene (1988) 73:409,Maeda et al., Nature (1985) 315:592-594, Lebacq-Verheyden et al., Mol.Cell. Biol. (1988) 8:3129; Smith et al., Proc. Natl. Acad. Sci. (USA)(1985) 82:8404, Miyajima et al., Gene (1987) 58:273; and Martin et al.,DNA (1988) 7:99. Numerous baculoviral strains and variants andcorresponding permissive insect host cells from hosts are described inLuckow et al., Bio/Technology (1988) 6:47-55, Miller et al., GenericEngineering (Setlow, J. K. et al. eds.), Vol. 8 (Plenum Publishing,1986), pp. 277-279, and Maeda et al., Nature, (1985) 315:592-594.

Mammalian Cells. Mammalian expression is accomplished as described inDijkema et al., EMBO J. (1985) 4:761, Gorman et al., Proc. Natl. Acad.Sci. (USA) (1982) 79:6777, Boshart et al., Cell (1985) 41:521 and U.S.Pat. No. 4,399,216. Other features of mammalian expression arefacilitated as described in Ham and Wallace, Meth. Enz. (1979) 58:44,Barnes and Sato, Anal. Biochem. (1980) 102:255, U.S. Pat. Nos.4,767,704, 4,657,866, 4,927,762, 4,560,655, WO 90/103430, WO 87/00195,and U.S. RE 30,985.

Screening Assays to Identify Chemotherapeutic Agents

The invention also encompasses screening assays to identify agents thatmodulate TTK activity, specifically that decrease aberrant TTK activityin an affected cell, e.g., a cancerous or pre-cancerous cell in whichTTK is differentially expressed. Such assays may be performed either invitro or in vivo.

Candidate Agents

The term “agent” as used herein describes any molecule with thecapability of altering the expression or physiological function of agene product of a differentially expressed gene. Generally a pluralityof assay mixtures are run in parallel with different agentconcentrations to obtain a differential response to the variousconcentrations. Typically, one of these concentrations serves as anegative control, i.e., at zero concentration or below the level ofdetection.

Candidate agents encompass numerous chemical classes, including, but notlimited to, organic molecules (e.g., small organic compounds having amolecular weight of more than 50 and less than about 2,500 daltons),peptides, monoclonal antibodies, antisense polynucleotides, andribozymes, and the like. Candidate agents can comprise functional groupsnecessary for structural interaction with proteins, particularlyhydrogen bonding, and typically include at least an amine, carbonyl,hydroxyl or carboxyl group, preferably at least two of the functionalchemical groups. The candidate agents often comprise cyclical carbon orheterocyclic structures and/or aromatic or polyaromatic structuressubstituted with one or more of the above functional groups. Candidateagents are also found among biomolecules including, but not limited to:polynucleotides, peptides, saccharides, fatty acids, steroids, purines,pyrimidines, derivatives, structural analogs or combinations thereof.

Candidate agents are obtained from a wide variety of sources includinglibraries of synthetic or natural compounds. For example, numerous meansare available for random and directed synthesis of a wide variety oforganic compounds and biomolecules, including expression of randomizedoligonucleotides and oligopeptides. Alternatively, libraries of naturalcompounds in the form of bacterial, fungal, plant and animal extractsare available or readily produced. Additionally, natural orsynthetically produced libraries and compounds are readily modifiedthrough conventional chemical, physical and biochemical means, and maybe used to produce combinatorial libraries. Known pharmacological agentsmay be subjected to directed or random chemical modifications, such asacylation, alkylation, esterification, amidification, etc. to producestructural analogs. Candidate agents can be assessed for modulation ofTTK activity either singly or in pools.

Screening of Candidate Agents In Vitro

A wide variety of in vitro assays may be used to screen candidate agentsfor the desired biological activity, including, but not limited to,labeled in vitro protein-protein binding assays, protein-DNA bindingassays (e.g., to identify agents that affect expression),electrophoretic mobility shift assays, imnuunoassays for proteinbinding, and the like. For example, by providing for the production oflarge amounts of a differentially expressed polypeptide, one canidentify ligands or substrates that bind to, modulate or mimic theaction of the polypeptide. Further methods for identifying these ligandsand substrates are provided below. The purified polypeptide may also beused for determination of three-dimensional crystal structure, which canbe used for modeling intermolecular interactions, transcriptionalregulation, etc.

The screening assay can be a binding assay, wherein one or more of themolecules may be joined to a label, and the label directly or indirectlyprovide a detectable signal. Various labels include radioisotopes,fluorescers, chemiluminescers, enzymes, specific binding molecules,particles, e.g., magnetic particles, and the like. Specific bindingmolecules include pairs, such as biotin and streptavidin, digoxin andantidigoxin etc. For the specific binding members, the complementarymember would normally be labeled with a molecule that provides fordetection, in accordance with known procedures.

A variety of other reagents may be included in the screening assaysdescribed herein. Where the assay is a binding assay, these includereagents like salts, neutral proteins, e.g., albumin, detergents, etcthat are used to facilitate optimal protein-protein binding, protein-DNAbinding, and/or reduce non-specific or background interactions. Reagentsthat improve the efficiency of the assay, such as protease inhibitors,nuclease inhibitors, anti-microbial agents, etc. may be used. Themixture of components are added in any order that provides for therequisite binding. Incubations are performed at any suitabletemperature, typically between 4 and 40° C. Incubation periods areselected for optimum activity, but may also be optimized to facilitaterapid high-throughput screening. Typically between 0.1 and 1 hours willbe sufficient.

Many mammalian genes have homologs in yeast and lower animals. The studyof such homologs physiological role and interactions with other proteinsin vivo or in vitro can facilitate understanding of biological function.In addition to model systems based on genetic complementation, yeast hasbeen shown to be a powerful tool for studying protein-proteininteractions through the two hybrid system described in Chien et al.1991 Proc. Natl. Acad. Sci. USA 88:9578-9582.

Screening of Candidate Agents In Vivo

Candidate agents can be screened in a non-human animal model of cancer(e.g., in animals into which have been injected cancerous cells; inanimals that are transgenic for an alteration in expression of adifferentially expressed gene as described herein, e.g., a transgenic“knock-out,” or a transgenic “knock-in,” a polynucleotide encoding allor a portion of a differentially expressed gene product and comprisingan operably linked reporter gene, and the like).

In general, the candidate agent is administered to the animal, and theeffects of the candidate agent determined. The candidate agent can beadministered in any manner desired and/or appropriate for delivery ofthe agent in order to effect a desired result. For example, thecandidate agent can be administered by injection (e.g., by injectionintravenously, intramuscularly, subcutaneously, or directly into thetissue in which the desired affect is to be achieved), orally, or by anyother desirable means. Normally, the in vivo screen will involve anumber of animals receiving varying amounts and concentrations of thecandidate agent (from no agent to an amount of agent hat approaches anupper limit of the amount that can be delivered successfully to theanimal), and may include delivery of the agent in different formulation.The agents can be administered singly or can be combined in combinationsof two or more, especially where administration of a combination ofagents may result in a synergistic effect.

The effect of agent administration upon the transgenic animal can bemonitored by assessing expression of the gene product, growth of theinjected tumor cells, and the like.

Identified Candidate Agents

Compounds having the desired pharmacological activity may beadministered in a physiologically acceptable carrier to a host fortreatment of a condition that is amenable to treatment by modulation ofexpression of a differentially expressed gene product. The therapeuticagents may be administered in a variety of ways, orally, topically,parenterally e.g., subcutaneously, intraperitoneally, by viralinfection, intravascularly, etc. Oral and inhaled treatments are ofparticular interest. Depending upon the manner of introduction, thecompounds may be formulated in a variety of ways. The concentration oftherapeutically active compound in the formulation may vary from about0.1-100 wt. %. The therapeutic agents can be administered in a singledose, or as multiple doses over a course of treatment.

The pharmaceutical compositions can be prepared in various forms, suchas granules, tablets, pills, suppositories, capsules, suspensions,salves, lotions and the like. Pharmaceutical grade organic or inorganiccarriers and/or diluents suitable for oral and topical use can be usedto make up compositions containing the therapeutically-active compounds.Diluents known to the art include aqueous media, vegetable and animaloils and fats. Stabilizing agents, wetting and emulsifying agents, saltsfor varying the osmotic pressure or buffers for securing an adequate pHvalue, and skin penetration enhancers can be used as auxiliary agents.

Methods of Screening for Drugs that Modulate TTK Activity

A TTK polypeptide or TTK-encoding nucleic acid according to the presentinvention may be used in screening for molecules which affect ormodulate TTK activity or function. Such molecules may be useful in atherapeutic and/or prophylactic context. Means for screening forsubstances potentially useful in treating or preventing cancer isprovided by the present invention. In general, the methods of theinvention are to facilitate identification of modulators of TTK activity(e.g., by modulating activity of TTK polypeptide or other TTK geneproduct, or by affecting TTK activity by targeting activity of geneproducts that act either upstream or downstream of TTK in a cascade thatleads to TTK activity), with agents that decrease TTK activity generallybeing of particular interest. Substances identified as modulators of theTTK activity represent an advance in the fight against cancer since theyprovide basis for design and investigation of pharmaceuticals for invivo use.

A method of screening for a substance which modulates activity of apolypeptide may include contacting one or more test substances with thepolypeptide in a suitable reaction medium, testing the activity of thetreated polypeptide (e.g., the ability to phosphorylate its substrate)and comparing that activity with the activity of the polypeptide incomparable reaction medium untreated with the test substance orsubstances. A difference in activity between the treated and untreatedpolypeptides is indicative of a modulating effect of the relevant testsubstance or substances.

Combinatorial library technology provides an efficient way of testing apotentially vast number of different substances for ability to modulateactivity of a polypeptide. Such libraries and their use are known in theart. The use of peptide libraries is preferred. Test substances may alsobe screened for ability to interact with the polypeptide, e.g., in ayeast two-hybrid system. This may be used as a coarse screen prior totesting a substance for actual ability to modulate activity of thepolypeptide. Alternatively, the screen could be used to screen testsubstances for binding to a TTK specific binding partner.

A substance identified using as a modulator of TTK polypeptide functionmay be peptide or non-peptide in nature. Non-peptide “small molecules”are often preferred for many in vivo pharmaceutical uses. Accordingly, amimetic or mimic of the substance (particularly if a peptide) may bedesigned for pharmaceutical use.

TTK Activity Assays

The activity of the TTK may be measured using any suitable kinase assayknown in the art. For example, and not by way of limitation, the methodsdescribed in Hogg et al (Oncogene 1994 9:98-96), Mills et al (J. Biol.Chem. 1992 267:16000-006) and Tomizawa et al 2001 (FEBS Lett. 2001 492:221-7), Schmandt et al, (J. Immunol. 1994, 152:96-105) may be used.Further serine, threonine and tyrosine kinase assays are described inAusubel et al. (Short Protocols in Molecular Biology, 1999, unit 17.6).

TTK assays generally use TTK polypeptide, a labeled donor substrate, anda receptor substrate that is either specific or non-specific for TTK. Insuch assays TTK transfers a labeled moiety from the donor substrate tothe receptor substrate, and kinase activity is measured by the amount oflabeled moiety transferred from the donor substrate to the receptorsubstrate.

TTK polypeptide may be produced using various expression systems asdetailed above, may be purified from cells, may be in the form of acleaved or uncleaved recombinant fusion protein and may have non-TTKpolypeptide sequences, for example a His tag or β-galactosidase at itsN- or C-terminus. TTK activity may be assayed in cancerous cells linesif the cancerous cell lines are used as a source of the TTK to beassayed. Suitable donor substrates for TTK assays include any moleculethat is susceptible to dephosphorylation by TTK include γ-labeled ATPand ATP analogs, wherein the label is ³³P, ³²P, ³⁵S or any otherradioactive isotope or a suitable fluorescent marker. Suitable recipientsubstrates for TTK assays include any polypeptide or other molecule thatis susceptible to phosphorylation by TTK. Recipient substrates areusually derived from fragments of in vivo targets of TTK. Recipientsubstrates fragments may be 8 to 50 amino acids in length, usually 10 to30 amino acids and preferably of about 10, 12, 15, 18, 20 and 25 aminoacids in length Further recipient substrates can be determinedempirically using a set of different polypeptides or other molecules.Targets of TTK suitable for TTK assays include tau and cdc25. Recipientsubstrates for TTK are typically capable of being purified from othercomponents of the reaction once the reaction has been performed. Thispurification is usually done through a molecular interaction, where therecipient substrates is biotinylated and purified through itsinteraction with streptavidin, or a specific antibody is available thatcan specifically recognize the recipient substrates. The reaction can beperformed in a variety of conditions, such as on a solid support, in agel, in solution or in living cells.

One exemplary recipient substrate for TTK phosphorylation is the humanprotein cdc25, SEQ ID NO:26, which is phosphorylated by TTK at theserine residues of amino acid position 214 and 216. Two fragments ofcdc25 are used as substrates in the kinase assay described below. Thesefragments comprise peptides A (SEQ ID NO:27), corresponding to aminoacids 209 to 225 of the cdc25 polypeptide sequence or peptide B (SEQ IDNO:28), corresponds to amino acids 210 to 223 of the cdc25 polypeptide.In this assay, two biotinylated polypeptides of comprising either SEQ IDNO:27 (Biotin-SGSGSGLYRSPSMPENLNRPR—NH2) or SEQ ID NO:28(Biotin-GGGGLYRSPSMPENLNRK-OH) are used.

The choice of detection methods depends on type of label used for thedonor molecule and may include, for example, measurement of incorporatedradiation or fluorescence by autoradiography, scintillation, scanning orfluorography.

Methods of Inhibiting Tumor Growth and Other Treatment Goals

The invention further provides methods for reducing growth of cancercells, particular breast or colon cancer cells. In general, the methodscomprise contacting a cancer cell that expresses TTK at an aberrantlevel relative to normal cells with a substance that (1) modulates,generally decreases, expression of TTK (e.g., a antisense polynucleotidecorresponding to TTK); or (2) otherwise modulates, generally decreases,TTK polypeptide levels and/or TTK activity in a cancerous cell havingaberrant TTK activity.

“Reducing growth of a cancer cell” includes, but is not limited to,reducing proliferation of cancer cells, and reducing the incidence of anormal cell from developing a cancerous phenotype or morphology. Whethera reduction in cancer cell growth has been achieved can be readilydetermined using any known assay, including, but not limited to,[³H]-thymidine incorporation; counting cell number over a period oftime; detecting, measuring a marker associated with colon cancer (e.g.,CEA, CA 19-9, and LASA), and/or methods well known in the art forassessing tumor burden.

The present invention provides methods for treating cancer (particularlybreast and colon cancer or other cancer that is associated withaberrantly high TTK activity) which methods generally compriseadministering to an individual an agent that reduces TTK activity in anamount sufficient to reduce cancer cell growth to treat the cancer.Whether a substance, or a specific amount of the substance, is effectivein treating cancer can be assessed using any of a variety of knowndiagnostic assays, e.g. in the case of colon cancer, sigmoidoscopy,proctoscopy, rectal examination, colonoscopy with biopsy, contrastradiographic studies, CAT scans, angiography, and detection of a tumormarker associated with colon cancer in the blood of the individual. Thesubstance can be administered systemically or locally. Thus, in someembodiments, the substance is administered locally, and colon cancergrowth is decreased at the site of administration. Local administrationmay be useful in treating, e.g., a solid tumor.

In one embodiment, the invention features polynucleotides that act asantisense polynucleotides and decrease TTK activity. Antisense TTKpolynucleotides generally comprise a polynucleotide of at least about 20to 3000 nucleotides, usually at least about 20 to 1000 nucleotides andmore usually at least about 8 to 50 nucleotides, and preferably about26, 20, 18, 17, 15, 10 and 8 nucleotides. Exemplary TTK polynucleotidesare provided in the Examples and in SEQ ID NO: 1-12, although anyantisense fragment of SEQ ID NO: 13 will suffice.

The therapeutic regimen is selected according to the expression profile.For example, if a patient's tumor indicates that the tumor producesaberrantly high level of TTK relative to normal cells, then a drughaving efficacy in the treatment of such TTK-expressing tumors isselected for therapy of that patient.

Pharmaceutical Compositions

Pharmaceutical compositions of the invention can comprise atherapeutically effective amount of a polypeptide, antibody,polynucleotide (including antisense nucleotides and ribozymes), or smallmolecule or other compound identified as modulating activity of TTK,preferably decreasing TTK activity. The term “therapeutically effectiveamount” as used herein refers to an amount of a therapeutic agent totreat, ameliorate, or prevent a desired disease or condition, or toexhibit a detectable therapeutic or preventative effect. The effect canbe detected by, for example, chemical markers or antigen levels.Therapeutic effects also include reduction in physical symptoms, such asdecreased body temperature, and/or in the effect upon tumor load in thesubject (e.g., decrease in tumor size or inhibition in tumor growth).The precise effective amount for a subject will depend upon thesubject's size and health, the nature and extent of the condition, andthe therapeutics or combination of therapeutics selected foradministration. Thus, it is not useful to specify an exact effectiveamount in advance. However, the effective amount for a given situationis determined by routine experimentation and is within the judgment ofthe clinician. For purposes of the present invention, an effective dosewill generally be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg toabout 10 mg/kg of the DNA constructs in the individual to which it isadministered.

A pharmaceutical composition can also contain a pharmaceuticallyacceptable carrier. The term “pharmaceutically acceptable carrier”refers to a carrier for administration of a therapeutic agent, such asantibodies or a polypeptide, genes, and other therapeutic agents. Theterm refers to any pharmaceutical carrier that does not itself inducethe production of antibodies harmful to the individual receiving thecomposition, and which can be administered without undue toxicity.Suitable carriers can be large, slowly metabolized macromolecules suchas proteins, polysaccharides, polylactic acids, polyglycolic acids,polymeric amino acids, amino acid copolymers, and inactive virusparticles. Such carriers are well known to those of ordinary skill inthe art. Pharmaceutically acceptable carriers in therapeuticcompositions can include liquids such as water, saline, glycerol andethanol. Auxiliary substances, such as wetting or emulsifying agents, pHbuffering substances, and the like, can also be present in suchvehicles. Typically, the therapeutic compositions are prepared asinjectables, either as liquid solutions or suspensions; solid formssuitable for solution in, or suspension in, liquid vehicles prior toinjection can also be prepared. Liposomes are included within thedefinition of a pharmaceutically acceptable carrier. Pharmaceuticallyacceptable salts can also be present in the pharmaceutical composition,e.g., mineral acid salts such as hydrochlorides, hydrobromides,phosphates, sulfates, and the like; and the salts of organic acids suchas acetates, propionates, malonates, benzoates, and the like. A thoroughdiscussion of pharmaceutically acceptable excipients is available inRemington 's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991). Theprecise nature of the carrier or other material may depend on the routeof administration, e.g., oral, intravenous, cutaneous or subcutaneous,nasal, intramuscular, intraperitoneal routes.

Pharmaceutical compositions for oral administration may be in tablet,capsule, powder or liquid form. A tablet may include a solid carriersuch as gelatin or an adjuvant. Liquid pharmaceutical compositionsgenerally include a liquid carrier such as water, petroleum, animal orvegetable oils, mineral oil or synthetic oil. Physiological salinesolution, dextrose or other saccharide solution or glycols such asethylene glycol, propylene glycol or polyethylene glycol may beincluded.

For intravenous, cutaneous or subcutaneous injection, or injection atthe site of affliction, the active ingredient will be in the form of aparenterally acceptable aqueous solution which is has suitable pH,isotonicity and stability. Suitable solutions, for example, optionallyinclude but are not limited to isotonic vehicles such as sodiumchloride, preservatives, stabilizers, buffers, antioxidants and/or otheradditives as required.

Administration of the pharmaceutical is administered in aprophylactically effective amount or a therapeutically effective amount.The actual amount administered, and rate and time-course ofadministration, will depend on the nature and severity of what is beingtreated. Decisions on dosage etc, can be determined by one skilled inthe art based upon the disclosed methods, and typically takes account ofthe disorder to be treated, the condition of the individual patient, thesite of delivery, the method of administration and other factors knownto practitioners. Examples of the techniques and protocols mentionedabove can be found in Remington's Pharmaceutical Sciences, 16th edition,Osol, A. (ed), 1980.

Alternatively, targeting therapies may be used to deliver the activeagent more specifically to certain types of cell, by the use oftargeting systems such as antibody or cell specific ligands. Targetingmay be desirable for a variety of reasons; for example if the agent isunacceptably toxic, or if it would otherwise require too high a dosage,or if it would not otherwise be able to enter the target cells.Targeting can be accomplished by, for example, administering adrug-antibody complex to a subject, wherein the antibody is specific fora cancer-associated antigen, and the drug is one that reduces cancercell growth. Targeting can be accomplished by coupling (e.g., linking,directly or via a linker molecule, either covalently or non-covalently,so as to form a drug-antibody complex) a drug to an antibody specificfor a cancer-associated antigen. Methods of coupling a drug to anantibody are well known in the art and need not be elaborated uponherein.

Pharmaceutical agents can also be produced in the target cells byexpression from an encoding gene introduced into the cells, e.g., in aviral or liposomal vector. The vector could be targeted to the specificcells to be treated, or it could contain regulatory elements which areswitched on more or less selectively by the target cells.

Alternatively, the agent could be administered in a precursor form, forconversion to the active form by an activating agent produced in, ortargeted to, the cells to be treated. A composition may be administeredalone or in combination with other treatments, either simultaneously orsequentially dependent upon the condition to be treated.

Delivery Methods for Therapy

Once formulated, the compositions of the invention or identified usingthe methods of the invention can be administered directly to the subject(e.g., as polynucleotide or polypeptides). Direct delivery of thecompositions will generally be accomplished by parenteral injection,e.g., subcutaneously, intraperitoneally, intravenously orintramuscularly, intratumoral or to the interstitial space of a tissue.Other modes of administration include oral and pulmonary administration,suppositories, and transdermal applications, needles, and gene guns orhyposprays. Dosage treatment can be a single dose schedule or a multipledose schedule.

Once a gene corresponding to a polynucleotide of the invention has beenfound to correlate with a proliferative disorder, such as neoplasia,dysplasia, and hyperplasia, the disorder can be amenable to treatment byadministration of a therapeutic agent based on the providedpolynucleotide, corresponding polypeptide or other correspondingmolecule (e.g., antisense, ribozyme, etc.).

The dose and the means of administration are determined based on thespecific qualities of the therapeutic composition, the condition, age,and weight of the patient, the progression of the disease, and otherrelevant factors. For example, administration of polynucleotidetherapeutic compositions agents of the invention includes local orsystemic administration, including injection, oral administration,particle gun or catheterized administration, and topical administration.Preferably, the therapeutic polynucleotide composition contains anexpression construct comprising a promoter operably linked to apolynucleotide of at least 12, 15, 17, 18, 22, 25, 30, or 35contiguous-nucleotides of the polynucleotide disclosed herein. Variousmethods can be used to administer the therapeutic composition directlyto a specific site in the body. For example, a small metastatic lesionis located and the therapeutic composition injected several times inseveral different locations within the body of tumor. Alternatively,arteries which serve a tumor are identified, and the therapeuticcomposition injected into such an artery, in order to deliver thecomposition directly into the tumor. A tumor that has a necrotic centeris aspirated and the composition injected directly into the now emptycenter of the tumor. The antisense composition is directly administeredto the surface of the tumor, for example, by topical application of thecomposition. X-ray imaging is used to assist in certain of the abovedelivery methods.

Receptor-mediated targeted delivery of therapeutic compositionscontaining an antisense polynucleotide, subgenomic polynucleotides, orantibodies to specific tissues can also be used. Receptor-mediated DNAdelivery techniques are described in, for example, Findeis et al.,Trends Biotechnol. (1993) 11:202; Chiou et al., Gene Therapeutics:Methods And Applications Of Direct Gene Transfer (J. A. Wolff, ed.)(1994); Wu et al., J. Biol. Chem. (1988) 263:621; Wu et al., J. Biol.Chem. (1994) 269:542; Zenke et al., Proc. Natl. Acad. Sci. (USA) (1990)87:3655; Wu et al., J. Biol. Chem. (1991) 266:338. Therapeuticcompositions containing a polynucleotide are administered in a range ofabout 100 ng to about 200 mg of DNA for local administration in a genetherapy protocol. Concentration ranges of about 500 ng to about 50 mg,about 1 μg to about 2 mg, about 5 μg to about 500 μg, and about 20 μg toabout 100 μg of DNA can also be used during a gene therapy protocol.Factors such as method of action (e.g., for enhancing or inhibitinglevels of the encoded gene product) and efficacy of transformation andexpression are considerations which will affect the dosage required forultimate efficacy of the antisense subgenomic polynucleotides. Wheregreater expression is desired over a larger area of tissue, largeramounts of antisense subgenomic polynucleotides or the same amountsreadministered in a successive protocol of administrations, or severaladministrations to different adjacent or close tissue portions of, forexample, a tumor site, may be required to effect a positive therapeuticoutcome. In all cases, routine experimentation in clinical trials willdetermine specific ranges for optimal therapeutic effect. Forpolynucleotide related genes encoding polypeptides or proteins withanti-inflammatory activity, suitable use, doses, and administration aredescribed in U.S. Pat. No. 5,654,173.

The therapeutic polynucleotides and polypeptides of the presentinvention can be delivered using gene delivery vehicles. The genedelivery vehicle can be of viral or non-viral origin (see generally,Jolly, Cancer Gene Therapy (1994) 1:51; Kimura, Human Gene Therapy(1994) 5:845; Connelly, Human Gene Therapy (1995) 1:185; and Kaplitt,Nature Genetics (1994) 6:148). Expression of such coding sequences canbe induced using endogenous mammalian or heterologous promoters.Expression of the coding sequence can be either constitutive orregulated.

Viral-based vectors for delivery of a desired polynucleotide andexpression in a desired cell are well known in the art. Exemplaryviral-based vehicles include, but are not limited to, recombinantretroviruses (see, e.g., WO 90/07936; WO 94/03622; WO 93/25698; WO93/25234; U.S. Pat. No. 5,219,740; WO 93/11230; WO 93/10218; U.S. Pat.No. 4,777,127; GB Patent No. 2,200,651; EP 0 345 242; and WO 91/02805),alphavirus-based vectors (e.g., Sindbis virus vectors, Semliki forestvirus (ATCC VR-67; ATCC VR-1247), Ross River virus (ATCC VR-373; ATCCVR-1246) and Venezuelan equine encephalitis virus (ATCC VR-923; ATCCVR-1250; ATCC VR 1249; ATCC VR-532), and adeno-associated virus (AAV)vectors (see, e.g., WO 94/12649, WO 93/03769; WO 93/19191; WO 94/28938;WO 95/11984 and WO 95/00655). Administration of DNA linked to killedadenovirus as described in Curiel, Hum. Gene Ther. (1992) 3:147 can alsobe employed.

Non-viral delivery vehicles and methods can also be employed, including,but not limited to, polycationic condensed DNA linked or unlinked tokilled adenovirus alone (see, e.g., Curiel, Hum. Gene Ther. (1992)3:147); ligand-linked DNA (see, e.g., Wu, J. Biol. Chem. (1989)264:16985); eukaryotic cell delivery vehicles cells (see, e.g., U.S.Pat. No. 5,814,482; WO 95/07994; WO 96/17072; WO 95/30763; and WO97/42338) and nucleic charge neutralization or fusion with cellmembranes. Naked DNA can also be employed. Exemplary naked DNAintroduction methods are described in WO 90/11092 and U.S. Pat. No.5,580,859. Liposomes that can act as gene delivery vehicles aredescribed in U.S. Pat. No. 5,422,120; WO 95/13796; WO 94/23697; WO91/14445; and EP 0524968. Additional approaches are described in Philip,Mol. Cell Biol. (1994) 14:2411, and in Woffendin, Proc. Natl. Acad. Sci.(1994) 91:1581.

Further non-viral delivery suitable for use includes mechanical deliverysystems such as the approach described in Woffendin et al., Proc. Natl.Acad. Sci. USA (1994) 91(24): 11581. Moreover, the coding sequence andthe product of expression of such can be delivered through deposition ofphotopolymerized hydrogel materials or use of ionizing radiation (see,e.g., U.S. Pat. No. 5,206,152 and WO 92/11033). Other conventionalmethods for gene delivery that can be used for delivery of the codingsequence include, for example, use of hand-held gene transfer particlegun (see, e.g., U.S. Pat. No. 5,149,655); use of ionizing radiation foractivating transferred gene (see, e.g., U.S. Pat. No. 5,206,152 and WO92/11033).

As an alternative to the use of viral vectors other known methods ofintroducing nucleic acid into cells includes electroporation, calciumphosphate co-precipitation, mechanical techniques such asmicroinjection, transfer mediated by liposomes and direct DNA uptake andreceptor-mediated DNA transfer. Gene transfer techniques whichselectively target the TTK nucleic acid to the affected cell type arepreferred. Examples of this included receptor-mediated gene transfer, inwhich the nucleic acid is linked to a protein ligand via polylysine,with the ligand being specific for a receptor present on the surface ofthe target cells.

Screening for Substances Affecting TTK Expression

The present invention also provides the use of all or part of thenucleic acid sequence of the TTK promoter and/or enhancer regions inmethods of screening for substances which modulate the activity of thepromoter and increase or decrease the level of TTK expression. Thisassay can be performed to identify anti-cancer agents for therapeuticand/or prophylactic purposes. The level of promoter activity, i.e., theability to initiate transcription, is quantifiable for instance byassessment of the amount of mRNA produced by transcription from thepromoter or by assessment of the amount of protein product produced bytranslation of mRNA produced by transcription from the promoter. Theamount of a specific mRNA present in an expression system may bedetermined for example using specific oligonucleotides which are able tohybridize with the mRNA and which are labeled or may be used in aspecific amplification reaction such as PCR. Use of a reporter genefacilitates determination of promoter activity by reference to proteinproduction.

Generally, a reporter gene under control of the TTK promoter and/orenhancers may be transcribed into mRNA which may be translated into apeptide or polypeptide product which may be detected and preferablyquantitated following expression. The reporter gene preferably encodesan enzyme which catalyses a reaction which produces a detectable signal,preferably a visually detectable signal, such as a coloured product.Many examples are known, including β-galactosidase and luciferase.β-galactosidase activity may be assayed by production of blue color onsubstrate, the assay being by eye or by use of a spectrophotometer tomeasure absorbance. Fluorescence, for example that produced as a resultof luciferase activity, may be quantitated using a spectrophotometer.Radioactive assays may be used, for instance using choloramphenicolacetyltransferase, which may also be used in non-radioactive assays. Thepresence and/or amount of gene product resulting from expression fromthe reporter gene may be determined using a molecule able to bind theproduct, such as an antibody or fragment thereof. The binding moleculemay be labeled directly or indirectly using any standard technique.

Those skilled in the art are well aware of a multitude of possiblereporter genes and assay techniques which may be used to determine geneactivity according to the presently disclosed methods. Any suitablereporter/assay may be used and the present invention is intended toencompass such systems.

Following identification of a substance which modulates or affectspromoter activity, the substance may be investigated further.Furthermore, it may be manufactured and/or used in preparation, i.e.manufacture or formulation, of a composition such as a medicament,pharmaceutical composition or drug.

Integrated Disease Information System

The levels of TTK in a sample can be used in an integrated diseaseinformation system to aid in analysis such as proposed patientinterventions, designing clinical trials, performing pharmacoeconomicanalysis, and illustrating disease progression for various patients overtime. For example, TTK information determined according to the methodsof the invention can be used in a system such as that described in U.S.Pat. No. 6,108,635 issued to Herren, et al. on Aug. 22, 2000. Such asystem can be for collecting the results of medical treatments given topatients in a plurality of locations. See, e.g., U.S. Pat. No. 5,713,350issued to Yokota, et al. on Feb. 3, 1998.

EXAMPLES

The following examples are put forth so as to provide those of ordinaryskill in the art with a complete disclosure and description of how tomake and use the present invention, and are not intended to limit thescope of what the inventors regard as their invention nor are theyintended to represent that the experiments below are all or the onlyexperiments performed. Efforts have been made to ensure accuracy withrespect to numbers used (e.g., amounts, temperature, etc.) but someexperimental errors and deviations should be accounted for. Unlessindicated otherwise, parts are parts by weight, molecular weight isweight average molecular weight, temperature is in degrees Centigrade,and pressure is at or near atmospheric.

Example 1 Source of Patient Tissue Samples

Normal and cancerous tissues were collected from patients using lasercapture microdissection (LCM) techniques, which techniques are wellknown in the art (see, e.g., Ohyama et al. (2000) Biotechniques29:530-6; Curran et al. (2000) Mol. Pathol. 53:64-8; Suarez-Quian et al.(1999) Biotechniques 26:328-35; Simone et al. (1998) Trends Genet14:272-6; Conia et al. (1997) J. Clin. Lab. Anal. 11:28-38; Emmert-Bucket al. (1996) Science 274:998-1001). Adenoma was not described in any ofthe patients; adenoma dysplasia (described as hyperplasia by thepathologist) was described in Patient ID No. 695. Extranodal extensionswere described in two patients, Patient ID Nos. 784 and 791.Lymphovascular invasion was described in seven patients, Patient ID Nos.128, 278, 517, 534, 784, 786, and 791. Crohn's-like infiltrates weredescribed in seven patients, Patient ID Nos. 52, 264, 268, 392, 393,784, and 791.

Example 2 Differential Expression of TTK

cDNA probes were prepared from total RNA isolated from the patient cellsdescribed in Example 1. Since LCM provides for the isolation of specificcell types to provide a substantially homogenous cell sample, thisprovided for a similarly pure RNA sample.

Total RNA was first reverse transcribed into cDNA using a primercontaining a T7 RNA polymerase promoter, followed by second strand DNAsynthesis. cDNA was then transcribed in vitro to produce antisense RNAusing the T7 promoter-mediated expression (see, e.g., Luo et al. (1999)Nature Med 5:117-122), and the antisense RNA was then converted intocDNA. The second set of cDNAs were again transcribed in vitro, using theT7 promoter, to provide antisense RNA. Optionally, the RNA was againconverted into cDNA, allowing for up to a third round of T7-mediatedamplification to produce more antisense RNA. Thus the procedure providedfor two or three rounds of in vitro transcription to produce the finalRNA used for fluorescent labeling. Fluorescent probes were generated byfirst adding control RNA to the antisense RNA mix, and producingfluorescently labeled cDNA from the RNA starting material. Fluorescentlylabeled cDNAs prepared from the tumor RNA sample were compared tofluorescently labeled cDNAs prepared from normal cell RNA sample. Forexample, the cDNA probes from the normal cells were labeled with Cy3fluorescent dye (green) and the cDNA probes prepared from the tumorcells were labeled with Cy5 fluorescent dye (red).

Each array used had an identical spatial layout and control spot set.Each microarray was divided into two areas, each area having an arraywith, on each half, twelve groupings of 32×12 spots for a total of about9,216 spots on each array. The two areas are spotted identically whichprovide for at least two duplicates of each clone per array. Spottingwas accomplished using PCR amplified products from 0.5 kb to 2.0 kb andspotted using a Molecular Dynamics Gen III spotter according to themanufacturer's recommendations. The first row of each of the 24 regionson the array had about 32 control spots, including 4 negative controlspots and 8 test polynucleotides. The test polynucleotides were spikedinto each sample before the labeling reaction with a range ofconcentrations from 2-600 pg/slide and ratios of 1:1. For each arraydesign, two sides were hybridized with the test samples reverse-labeledin the labeling reaction. This provided for about 4 duplicatemeasurements for each clone, two of one color and two of the other, foreach sample.

The differential expression assay was performed by mixing equal amountsof probes from tumor cells and normal cells of the same patient. Thearrays were prehybridized by incubation for about 2 hrs at 60° C. in5×SSC/0.2% SDS/1 mM EDTA, and then washed three times in water and twicein isopropanol. Following prehybridization of the array, the probemixture was then hybridized to the array under conditions of highstringency (overnight at 42° C. in 50% formamide, 5×SSC, and 0.2% SDS.After hybridization, the array was washed at 55° C. three times asfollows: 1) first wash in 1×SSC/0.2% SDS; 2) second wash in 0.1×SSC/0.2%SDS; and 3) third wash in 0.1×SSC.

The arrays were then scanned for green and red fluorescence using aMolecular Dynamics Generation III dual color laser-scanner/detector. Theimages were processed using BioDiscovery Autogene software, and the datafrom each scan set normalized to provide for a ratio of expressionrelative to normal. Data from the microarray experiments was analyzedaccording to the algorithms described in U.S. application No.60/252,358, filed Nov. 20, 2000, by E. J. Moler, M. A. Boyle, and F. M.Randazzo, and entitled “Precision and accuracy in cDNA microarray data,”which application is specifically incorporated herein by reference.

The experiment was repeated, this time labeling the two probes with theopposite color in order to perform the assay in both “color directions.”Each experiment was sometimes repeated with two more slides (one in eachcolor direction). The level fluorescence for each sequence on the arrayexpressed as a ratio of the geometric mean of 8 replicate spots/genesfrom the four arrays or 4 replicate spots/gene from 2 arrays or someother permutation. The data were normalized using the spiked positivecontrols present in each duplicated area, and the precision of thisnormalization was included in the final determination of thesignificance of each differential. The fluorescent intensity of eachspot was also compared to the negative controls in each duplicated areato determine which spots have detected significant expression levels ineach sample.

A statistical analysis of the fluorescent intensities was applied toeach set of duplicate spots to assess the precision and significance ofeach differential measurement, resulting in a p-value testing the nullhypothesis that there is no differential in the expression level betweenthe tumor and normal samples of each patient. During initial analysis ofthe microarrays, the hypothesis was accepted if p>10⁻³, and thedifferential ratio was set to 1.000 for those spots. All other spotshave a significant difference in expression between the tumor and normalsample. If the tumor sample has detectable expression and the normaldoes not, the ratio is truncated at 1000 since the value for expressionin the normal sample would be zero, and the ratio would not be amathematically useful value (e.g., infinity). If the normal sample hasdetectable expression and the tumor does not, the ratio is truncated to0.001, since the value for expression in the tumor sample would be zeroand the ratio would not be a mathematically useful value. These lattertwo situations are referred to herein as “on/off.” Database tables werepopulated using a 95% confidence level (p>0.05).

The difference in the expression level of TTK in the colon tumor cellsrelative to the matched normal colon cells was greater than or equal to2 fold (“>=2×”) in 39% of the patients, greater than or equal to 2.5fold in 36% of the patients, and greater than or equal to 5 fold in 27%of the patients examined.

Quantitative PCR of a number of normal tissues and tumor cell lines,particularly colorectal carcinoma cell lines was used to analyzeexpression of TTK. Quantitative real-time PCR was performed by firstisolating RNA from cells using a Roche RNA Isolation kit according tomanufacturer's directions. One microgram of RNA was used to synthesize afirst-strand cDNA using MMLV reverse transcriptase (Ambion) using themanufacturers buffer and recommended concentrations of oligo dT,nucleotides, and Rnasin. This first-strand cDNA served as a template forquantitative real-time PCR using the Roche light-cycler as recommendedin the machine manual. TTK was amplified with the forward primerCGGAATCAAGTCTTCTAGCT (SEQ ID NO:1) and reverse primerGGTTGCTCAAAAGTTGGTATG (SEQ ID NO:2) PCR product was quantified based onthe cycle at which the amplification entered the linear phase ofamplification in comparison to an internal standard and using thesoftware supplied by the manufacturer. Small differences in amounts ortotal template in the first-strand cDNA reaction were eliminated bynormalizing to amount of actin amplified in a separate quantitative PCRreaction using the forward primer 5′-CGGGAAATCGTGCGTGACATTAAG-3′(SEQ IDNO:3) and the reverse primer: 5′-TGATCTCCTTCTGCATCCTGTCGG-3′ (SEQ IDNO:4). The results for TTK mRNA levels in normal tissues are shown inFIG. 1; the results for TTK mRNA levels in tumor cell lines are shown inFIG. 2. A brief description of the cell lines analyzed is provided inTable A below.

TABLE A Cell Line Tissue Source MDA-MB-231 Human breast; high metastaticpotential (micromets in lung; adenocarcinoma; pleural effusionMDA-MB-435 Human breast, high metastatic potential (macrometastases inlung) MCF-7 Human breast; non-metastatic MDA-MB-468 Human breast;adenocarcinoma Alab Human breast, metastatic SKOV3 Human ovarianadenocarcinoma OVCAR3 Human ovarian adenocarcinoma KM12C Human colon;low metastatic potential KM12L4 Human colon; high metastatic potential(derived from Km12C) DU 145 Human prostate; carcinoma; from metastaticsite: brain HT1080 Human sarcoma cell line; HMVEC Primary humanmicrovascular endothelial cells 184B5 normal breast epithelial cells;chemically transformed LNCAP prostate carcinoma; metastasis to leftsupraclavicular lymph U373MG glioblastoma cell WOCA primary prostateepithelium Caco-2 Human colorectal adenocarcinoma SW620 Human colorectaladenocarcinoma; from metastatic site (lymph node) LS174T High metastaticpotential human colorectal adenocarcinoma LOVO Human colorectaladenocarcinoma; colon; from metastatic site (colon) HT29 Humancolorectal adenocarcinoma; colon SW480 Human colorectal adenocarcinoma;colon HCT116 Human colorectal carcinoma; colon Colo 320DN Humancolorectal adenocarcinoma; colon T84 Human colorectal carcinoma; colon;from metastatic site (lung) HCT15 Human colorectal adenocarcinoma; colonCCD112 Human colorectal adenocarcinoma, low metastatic potential DLD1Human colon; colorectal adenocarcinoma 293 kidney epithelial cells GRDP2primary prostate epithelium IMR90 primary lung fibroblast PC3 prostatecancer; androgen receptor negative

TTK was expressed in normal cells (FIG. 1), with thymus and testisidentified as the normal tissues that most highly express the gene forTTK. Numerous cancer cells, however, displayed a significantly elevatedlevel of TTK expression (FIG. 2) as compared to most wild-type tissues.

Example 3 Hierarchical Clustering and Stratification of Colon CancersUsing Differential Expression Data

Differential expression patterns from Example 2 were analyzed byapplying hierarchical clustering methods to the data sets (see Eisen etal. (1998) PNAS 95:14863-14868). In short, hierarchical clusteringalgorithms are based on the average-linkage method of Sokal and Michener(Sokal, RR & Michener, CD (1958) Univ. Kans. Sci. Bull. 38, 1409-1438),which was developed for clustering correlation matrixes. The object ofthis algorithm is to compute a dendrogram that assembles all elementsinto a single tree. For any set of n genes, an upper-diagonal similaritymatrix is computed which contains similarity scores for all pairs ofgenes. The matrix is scanned to identify the highest value (representinga similar pair of genes). Using this technique, four groups ofdifferential expression patterns were identified and assigned toclusters.

Application of hierarchical clustering to the data from Example 2revealed that IGF2 (insulin-like growth factor 2), TTK (serine,threonine, tyrosine kinase implicated in the cell cycle), MAPKAPK2(mitogen-activated protein (MAP) kinase-activated protein kinase), andMARCKS (myristoylated alanine-rich C kinase substrate, which is asubstrate of protein kinase C) are concurrently upregulated as detectedin 9 out of the 33 colon cancer patient samples examined. The data forthese experiments is presented in graphical form in FIGS. 3-6. Theconcurrent upregulation suggests that these genes are co-regulated andthat patients with an elevated serum level of IGF2 may be candidates fortreatment with inhibitors to TTK, MAPKAP kinase 2, MARCKS and/or IGF2.

Example 4 Antisense Regulation of TTK Expression

Additional functional information on TTK was generated using antisenseknockout technology. TTK expression in cancerous cells was furtheranalyzed to confirm the role and function of the gene product intumorgenesis, e.g., in promoting a metastatic phenotype.

A number of different oligonucleotides complementary to TTK mRNA weredesigned as potential antisense oligonucleotides, and tested for theirability to suppress expression of TTK. The ability of each designedantisense oligonucleotide to inhibit gene expression was tested throughtransfection into SW620 colon colorectal carcinoma cells. For eachtransfection mixture, a carrier molecule, preferably a lipitoid orcholesteroid, was prepared to a working concentration of 0.5 mM inwater, sonicated to yield a uniform solution, and filtered through a0.45 μm PVDF membrane. The antisense or control oligonucleotide was thenprepared to a working concentration of 100 μM in sterile Milliporewater. The oligonucleotide was further diluted in OptiMEM™ (Gibco/BRL),in a microfuge tube, to 2 μM, or approximately 20 μg oligo/ml ofOptiMEM™. In a separate microfuge tube, lipitoid or cholesteroid,typically in the amount of about 1.5-2 nmol lipitoid/μg antisenseoligonucleotide, was diluted into the same volume of OptiMEM™ used todilute the oligonucleotide. The diluted antisense oligonucleotide wasimmediately added to the diluted lipitoid and mixed by pipetting up anddown. Oligonucleotide was added to the cells to a final concentration of30 nM.

The level of target mRNA (TTK) in the transfected cells was quantitatedin the cancer cell lines using the Roche LightCycler™ real-time PCRmachine. Values for the target mRNA were normalized versus an internalcontrol (e.g., beta-actin). For each 20 μl reaction, extracted RNA(generally 0.2-1 μg total) was placed into a sterile 0.5 or 1.5 mlmicrocentrifuge tube, and water was added to a total volume of 12.5 μl.To each tube was added 7.5 μl of a buffer/enzyme mixture, prepared bymixing (in the order listed) 2.5 μl H₂O, 2.0 μl 10× reaction buffer, 10μl oligo dT (20 pmol), 1.0 μl dNTP mix (10 mM each), 0.5 μl RNAsin® (20u) (Ambion, Inc., Hialeah, Fla.), and 0.5 μl MMLV reverse transcriptase(50 u) (Ambion, Inc.). The contents were mixed by pipetting up and down,and the reaction mixture was incubated at 42° C. for 1 hour. Thecontents of each tube were centrifuged prior to amplification.

An amplification mixture was prepared by mixing in the following order:1×PCR buffer II, 3 mM MgCl₂, 140 μM each dNTP, 0.175 pmol each oligo,1:50,000 dil of SYBR® Green, 0.25 mg/ml BSA, 1 unit Taq polymerase, andH₂O to 20 μl. (PCR buffer II is available in 10× concentration fromPerkin-Elmer, Norwalk, Conn.). In 1× concentration it contains 10 mMTris pH 8.3 and 50 mM KCl. SYBR® Green (Molecular Probes, Eugene, Oreg.)is a dye which fluoresces when bound to double stranded DNA. As doublestranded PCR product is produced during amplification, the fluorescencefrom SYBR® Green increases. To each 20 μl aliquot of amplificationmixture, 2 μl of template RT was added, and amplification was carriedout according to standard protocols.

The following antisense oligonucleotides were shown to effectivelydeplete TTK RNA in the transfection assays:

Oligo 79-5AS: GGGACTCTTCCAAATGGGCATGACT (SEQ ID NO:5) Oligo 79-9AS:TGCAGTAACTCTTGCGTTCCCATGG (SEQ ID NO:6)

The reverse control of each of these antisense oligonucleotides weresynthesized, as were oligonucleotides with the identical sequence of theantisense oligonucleotides in reverse orientation (Reverse Control):

Oligo 79-5RC: TCAGTACGGGTAAACCTTCTCAGGG (SEQ ID NO:7) Oligo 79-9RC:GGTACCCTTGCGTTGTCAATGACCT (SEQ ID NO:8)

The antisense oligonucleotides were introduced into a test cell and theeffect upon TTK expression of the corresponding gene, as well as theeffect induction of the cancerous phenotype, was examined as describedbelow.

Example 5 Effect of TTK Expression on Proliferation

The effect of TTK on proliferation was assessed in metastatic breastcancer cell lines (MDA-MB-231 (“231”)), SW620 colon colorectal carcinomacells, or 847 human immortal fibroblast cells. Transfection was carriedout as described above in Example 4.

Cells were plated to approximately 60-80% confluency in 96-well dishes.Antisense or reverse control oligonucleotide was diluted to 2 μM inOptiMEM™ and added to OptiMEM™ into which the delivery vehicle, lipitoid116-6 in the case of SW620 cells or 1:1 lipitoid 1:cholesteroid 1 in thecase of MDA-MB-231 cells, had been diluted. The oligo/delivery vehiclemixture was then further diluted into medium with serum on the cells.The final concentration of oligonucleotide for all experiments was 300nM, and the final ratio of oligo to delivery vehicle for all experimentswas 1.5 nmol lipitoid/μg oligonucleotide. Cells were transfectedovernight at 37° C. and the transfection mixture was replaced with freshmedium the next morning.

Transfection of the antisense oligonucleotides into both SW620colorectal carcinoma cells (FIG. 7) and 231 cells (FIG. 8) resulted in adecreased rate of proliferation compared to matched reverse control (RC)and oligonucleotides, but no inhibition of growth of 847 human immortalfibroblast cells (FIG. 11), suggesting possible tissue or transformationspecificity in the functional role for the TTK protein.

Example 6 Effect of TTK Expression on Colony Formation

The effect of TTK expression upon colony formation was tested in a softagar assay. Soft agar assays were conducted by first establishing abottom layer of 2 ml of 0.6% agar in media plated fresh within a fewhours of layering on the cells. The cell layer was formed on the bottomlayer by removing cells transfected as described above from plates using0.05% trypsin and washing twice in media. The cells were counted in aCoulter counter, and resuspended to 10⁶ per ml in media. 10 μl aliquotsare placed with media in 96-well plates (to check counting with WST1),or diluted further for soft agar assay. 2000 cells are plated in 800 μl0.4% agar in duplicate wells above 0.6% agar bottom layer. After thecell layer agar solidifies, 2 ml of media is dribbled on top andantisense or reverse control oligo is added without delivery vehicles.Fresh media and oligos are added every 3-4 days. Colonies are formed in10 days to 3 weeks. Fields of colonies were counted by eye. Wst-1metabolism values can be used to compensate for small differences instarting cell number. Larger fields can be scanned for visual record ofdifferences.

As shown in FIG. 9, antisense oligonucleotides to TTK (79-9AS) led todecreased colony size and number compared to control reverse controloligonucleotides (79-9RC) or to control oligonucleotides (52-3AS:TAGGTCTTTGGCCGGTGATGGGTCG (SEQ ID NO:9) and 52-3RC:GCTGGGTAGTGGCCGGTTTCTGGAT (SEQ ID NO:10)). The 52-3 antisenseoligonucleotide is directed to the hD53 mRNA, and serves as a negativecontrol in the experiment.

Example 7 Induction of Cell Death Upon Depletion of TTK (“AntisenseKnockout”)

SW620 cells were transfected as described for proliferation assays. Forcytotoxic effect in the presence of cisplatin (cis), the same protocolwas followed but cells were left in the presence of 2 μM drug. Each day,cytotoxicity was monitored by measuring the amount of LDH enzymereleased in the medium due to membrane damage. The activity of LDH wasmeasured using the Cytotoxicity Detection Kit from Roche MolecularBiochemicals. The data is provided as a ratio of LDH released in themedium vs. the total LDH present in the well at the same time point andtreatment (rLDH/tLDH). A positive control using antisense and reversecontrol oligonucleotides for BCL2 (a known anti-apoptotic gene) showsthat loss of message for BCL2 leads to an increase in cell deathcompared with treatment with the control oligonucleotide (backgroundcytotoxicity due to transfection).

The following antisense oligonucleotides were tested for the ability todeplete the message levels of the gene corresponding to the indicatedcluster. Oligo Name: AS or RC provides the name of the target gene orname of the oligo, and whether the oligo is antisense (AS) or a reversecontrol (RC).

TABLE B Oligo Name:Antisense (AS) or Reverse Control (RC) Oligo SequenceSEQ ID NO: Chir39-5:AS ACTCATCTGGCTGGGCTATGGTGGT SEQ ID NO:11Chir39-5:RC TGGTGGTATCGGGTCGGTCTACTCA SEQ ID NO:12 Chir79-9:ASTCCAGTAACTCTTGCGTTCCCATGG SEQ ID NO:6 Chir79-9:RCGGTACCCTTGCGTTCTCAATGACCT SEQ ID NO:8

As shown in FIG. 12, Chiron 79-9 (TTK) antisense does not sensitize thecells to treatment by cisplatin at a detectable level, but leads toincreased death compared to control oligo at day 3.

Example 8 Sample Assay for Agents that Modulate TTK Activity

This assay may be performed in microtitre plates. TTK was purified as a6×His tagged fusion protein using a baculovirus expression system.Essentially 20 ul of 20 nM TTK (100 k Da) in TTK kinase buffercomprising 50 mM Hepes pH 7.4, 2 mM MgCl₂, 10 mM MnCl₂, 1 mM NaF, 50 mMNaCl, 1 mM DTT and 1 mg/ml BSA was added to 5 ul of a candidate agentdiluted in 20% DMSO, 10 ul of a 2.8 uM solution of a biotinylatedsubstrate peptide derived from cdc25, such asBiotin-SGSGSGLYRSPSMPENLNRPR-NH2 (SEQ ID NO:27) orBiotin-GGGGLYRSPSMPENLNRK-OH (SEQ ID NO:28) and 5 ul of 80 nM ³³P-γATPin a well of a microtitre plate. Samples were mixed, incubated for 2hours and each reaction is terminated using 20 ul of 0.5 M EDTA pH 8.0.50 ul of the sample is transferred to a 96 well flat bottom Streptavidincoated flash plate, and the sample is incubated with the plate for 1 hrat room temperature. The wells of the plate are washed four times with250 ul of calcium and magnesium-free phosphate buffered saline, andscintillation fluid is added to the sample. Activity of TTK was measuredby calculating the emission of ³³P, transferred by TTK from ³³P-γATP toa substrate peptide, by scintillation.

Agents modulating TTK activity can be identified by comparing theactivity of TTK in the presence of a candidate agent to the activity ofTTK in the absence of a candidate agent.

While the present invention has been described with reference to thespecific embodiments thereof, it should be understood by those skilledin the art that various changes may be made and equivalents may besubstituted without departing from the true spirit and scope of theinvention. In addition, many modifications may be made to adapt aparticular situation, material, composition of matter, process, processstep or steps, to the objective, spirit and scope of the presentinvention. All such modifications are intended to be within the scope ofthe invention.

1. A method of detecting colon or breast cancer expressing increasedlevels of TTK in a human subject, the method comprising: detecting alevel of expression of a TTK polynucleotide in a test sample obtainedfrom the subject, wherein the test sample is derived from tissue, tumor,blood, plasma, or serum; and comparing the level of expression of theTTK polynucleotide in the test sample to a level of expression in anormal non-cancer sample of the same type; wherein detection of anexpression level of TTK polynucleotide in the test sample that isincreased at least two fold relative to the level of expression in thenormal non-cancer sample indicates that the subject has colon or breastcancer expressing increased levels of TTK.
 2. The method of claim 1,wherein the test sample is a colon sample.
 3. The method of claim 1,wherein the test sample is a breast sample.
 4. The method of claim 1wherein the cancer is colon cancer.
 5. The method of claim 4 wherein thecolon cancer is familial adenomatous polyposis, Gardner's syndrome,hereditary nonpolyposis colon cancer or familial colorectal cancer. 6.The method of claim 1 wherein the cancer is a breast cancer selectedfrom the group consisting of ductal carcinoma in situ, infiltratingductal carcinoma, lobular carcinoma in situ, infiltrating lobularcarcinoma, inflammatory breast cancer, medullary carcinoma, mucinouscarcinoma, Paget's disease of the nipple, Phyllodes tumor, and tubularcarcinoma.
 7. The method of claim 1 wherein the expression level of TTKpolynucleotide in the test sample is increased at least 2.5 foldrelative to the level of expression in the normal non-cancer sample. 8.The method of claim 1 wherein the expression level of TTK polynucleotidein the test sample is increased at least 5 fold relative to the level ofexpression in the normal non-cancer sample.
 9. The method of claim 1further comprising detecting differential expression of at least one ofp53, DCC, ras, FAP, MAPKAPK2, MARCKS and IGF2 in the test sample. 10.The method of claim 9 wherein an upregulation of expression of at leastone of p53, DCC, ras, FAP, MAPKAPK2, MARCKS and IGF2 combined with anincrease in expression level of TTK polynucleotide is indicative ofcolon or breast cancer.
 11. The method of claim 9 wherein anupregulation of expression of p53, DCC, ras, FAP, MAPKAPK2, MARCKS andIGF2 combined with an increase in expression level of TTK polynucleotideis indicative of colon or breast cancer.
 12. The method of claim 1wherein TTK expression is detected by measuring TTK mRNA levels.
 13. Themethod of claim 1 wherein expression levels of TTK polynucleotide aremeasured using PCR or hybridization under stringent conditions, whereinsaid conditions comprise incubation at 42° C. in 50% formamide, 5×SSC,and 0.2% SDS.
 14. The method of claim 1 wherein the TTK polynucleotidecomprises a nucleotide sequence at least 95% identical to a sequence ofSEQ ID NO:13.
 15. The method of claim 1 wherein the TTK polynucleotidecomprises a nucleotide sequence at least 98% identical to a sequence ofSEQ ID NO:13.
 16. The method of claim 1 wherein the TTK polynucleotidecomprises the nucleotide sequence of SEQ ID NO:13.
 17. The method ofclaim 1 wherein the TTK polynucleotide comprises a nucleotide sequenceencoding at least 25 contiguous amino acids of SEQ ID NO:14.
 18. Themethod of claim 1 wherein the TTK polynucleotide comprises a nucleotidesequence comprising between 15 to 100 contiguous nucleotides of SEQ IDNO:13.
 19. The method of claim 14 wherein the nucleotide sequence atleast 95% identical to a sequence of SEQ ID NO:13 encodes a TTKpolypeptide with protein kinase activity.
 20. A method for determiningwhether cancerous tissue in a subject expresses increased levels of TTK,wherein the method comprises: detecting a level of expression of a TTKpolynucleotide in a cancerous tissue sample obtained from the subjectand comparing the level of expression of the TTK polynucleotide in thecancerous tissue sample to a level of expression in a normalnon-cancerous sample of the same tissue, wherein detection of anexpression level of TTK polynucleotide in the cancerous tissue samplethat is increased at least two fold relative to the level of expressionin the normal non-cancerous sample indicates that the subject hascancerous tissue expressing increased levels of TTK.
 21. The method ofclaim 20, wherein the tissue sample is a colon sample.
 22. The method ofclaim 20, wherein the tissue sample is a breast sample.
 23. The methodof claim 20 wherein the cancer is colon cancer.
 24. The method of claim20 wherein the colon cancer is familial adenomatous polyposis, Gardner'ssyndrome, hereditary nonpolyposis colon cancer or familial colorectalcancer.
 25. The method of claim 20 wherein the cancer is a breast cancerselected from the group consisting of ductal carcinoma in situ,infiltrating ductal carcinoma, lobular carcinoma in situ, infiltratinglobular carcinoma, inflammatory breast cancer, medullary carcinoma,mucinous carcinoma, Paget's disease of the nipple, Phyllodes tumor, andtubular carcinoma.
 26. The method of claim 20 wherein TTK expression isdetected by measuring TTK mRNA levels.
 27. The method of claim 20wherein the TTK polynucleotide comprises a nucleotide sequence at least95% identical to a sequence of SEQ ID NO:13.
 28. The method of claim 20wherein the TTK polynucleotide comprises a nucleotide sequence at least98% identical to a sequence of SEQ ID NO:13.
 29. The method of claim 20wherein the TTK polynucleotide comprises the nucleotide sequence of SEQID NO:13.
 30. The method of claim 20 wherein the TTK polynucleotidecomprises a nucleotide sequence encoding at least 25 contiguous aminoacids of SEQ ID NO:14.
 31. The method of claim 20 wherein the TTKpolynucleotide comprises a nucleotide sequence comprising between 15 to100 contiguous nucleotides of SEQ ID NO:13.
 32. The method of claim 27wherein the nucleotide sequence at least 95% identical to a sequence ofSEQ ID NO:13 encodes a TTK polypeptide with protein kinase activity.